# ent

id: cord-004502-3mkv3bal
type: GGP
entity:
  RER VCO 2 VO 2 f and physical avtivity h were measured simultaneously g Energy expenditure values adjusted for body weight using ANCOVA i Food


id: cord-004502-3mkv3bal
type: GGP
entity:
  Peroxisome proliferator activated receptorgamma coactivator 1 alpha PGC 1 alpha transcriptional coactivator and metabolic regulator PGC 1alpha


id: cord-004502-3mkv3bal
type: WORK_OF_ART
entity:
  Lipolysis in Brown Adipocytes Is Not Essential for Cold Induced Thermogenesis in Mice Cold Induced Thermogenesis


id: cord-021152-6znmkvy9
type: PROTEIN
entity:
  Coronaviridae family 19 20 21 22 Molecular evidence suggests that the Severe Acute Respiratory Syndrome Betacoronavirus SARS CoV beta CoV


id: cord-003166-k3jxvzfi
type: DNA
entity:
  bat paramyxovirus B16 40 10 5 75 TCID 50 mL and human parainfluenza virus 1 KBPV VR 44 10 5 75 TCID 50 mL


id: cord-003775-1axsebya
type: DISEASE
entity:
  Chordopoxviruses Avipoxvirus Capripoxvirus Centapoxvirus Cervidpoxvirus Crocodylidpoxvirus Leporipoxvirus Molluscipoxvirus Orthopoxvirus


id: cord-004510-cbutpjre
type: WORK_OF_ART
entity:
  The Serological Prevalence of Rabies Virus Neutralizing Antibodies in the Bat Population on the Caribbean Island


id: cord-004510-cbutpjre
type: ORG
entity:
  the Rapid Fluorescent Focus Inhibition Test for Measuring Rabies Virus Neutralizing Antibodies Protection of bats


id: cord-006502-6ajms947
type: PROTEIN
entity:
  angiotensinogen angiotensin converting enzyme ACE ACE2 renin pro renin receptor aldosterone angiotensin II type 1 AT1


id: cord-006502-6ajms947
type: DNA
entity:
  d i p o c y t o k i n e s i n c l u d i n g a d i p o n e c t i n l e p t i n adrenomedullin vascular endothelial growth factor VEGF angiotensinogen plasminogen activator inhibitor 1 PAI 1 resistin omentin apelin


id: cord-010307-sxh5mq1q
type: DNA
entity:
  Top End i Chalinolobus nigrogriseus Scotorepens greyii and Scotorepens sanborni ii Miniopterus schreibersii


id: cord-262434-q4tk96tq
type: CL
entity:
  red squirrels Sciurus vulgaris Temporal and serological findings An increasing danger of zoonotic orthopoxvirus


id: cord-255137-utg8k7qs
type: PROTEIN
entity:
  VIRSorter_NODE_210_length_3873_cov_4_79189 cat_1 VIRSorter_NODE_388_length_2881_cov_7_17939 cat_1 VIRSorter_NODE_5_length_42493_cov_21_423


id: cord-255137-utg8k7qs
type: DNA
entity:
  cat_1 VIRSorter_NODE_154_length_5846_cov_32_8156 cat_2 VIRSorter_NODE_2_length_40986_cov_83_5436 cat_2 VIRSorter_NODE_14_length_28627_cov_424_601 cat_2 VIRSorter_NODE_130_length_7398_cov_6_88034 cat_2 VIRSorter_NODE_911_length_1516_cov_2_82279 cat_2 VIRSorter_NODE_60_length_9439_cov_32_4934 cat_1 VIRSorter_NODE_98_length_5449_cov_11_7885 cat_1 VIRSorter_NODE_193_length_2388_cov_2_87797 cat_2 VIRSorter_NODE_25_length_14198_cov_12_3353 cat_2 VIRSorter_NODE_83_length_6779_cov_23_1462 cat_1 VIRSorter_NODE_37_length_8496_cov_10_6883 cat_1 VIRSorter_NODE_97_length_6417_cov_22_439 cat_2 VIRSorter_NODE_20_length_3093_cov_15_1522 cat_1 VIRSorter_NODE_794_length_2121_cov_3_72505 cat_2 VIRSorter_NODE_510_length_2453_cov_9_21212 cat_2 VIRSorter_NODE_11_length_24212_cov_31_2924 cat_1 VIRSorter_NODE_16_length_17400_cov_20_1101 cat_2 VIRSorter_NODE_1_length_45933_cov_26_6238 cat_1 VIRSorter_NODE_4_length_46625_cov_133_007 circular cat_1 VIRSorter_NODE_52_length_9386_cov_11_0833 cat_2


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
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id: cord-255137-utg8k7qs
type: DNA
entity:
  cat_1 VIRSorter_NODE_241_length_2048_cov_3_82192 cat_2 VIRSorter_NODE_566_length_1570_cov_4_87877 cat_1 VIRSorter_NODE_236_length_2071_cov_8_333 cat_2 VIRSorter_NODE_21_length_8643_cov_7_23897 cat_1 Halocynthia


id: cord-255137-utg8k7qs
type: DNA
entity:
  VIRSorter_NODE_572_length_1258_cov_4_2989 cat_2 VIRSorter_NODE_511_length_1714_cov_9_19609 cat_2 VIRSorter_NODE_105_length_2295_cov_5_80162_ID_209_GC022959_GC022959 cat_2 VIRSorter_NODE_351_length_1653_cov_3_89784 cat_2 VIRSorter_NODE_62_length_4317_cov_5_92123_GC022960_GC022960 cat_2 VIRSorter_NODE_70_length_5230_cov_7_68756 cat_1 VIRSorter_NODE_59_length_5445_cov_7_07004 cat_2 VIRSorter_NODE_151_length_2931_cov_21_0263 cat_2 VIRSorter_NODE_87_length_2972_cov_3_15406 cat_2


id: cord-255137-utg8k7qs
type: DNA
entity:
  VIRSorter_NODE_11_length_18974_cov_17_7842 cat_2 VIRSorter_NODE_2774_length_1414_cov_2_55497 cat_2 VIRSorter_NODE_250_length_2007_cov_4_84663


id: cord-255137-utg8k7qs
type: DNA
entity:
  VIRSorter_NODE_46_length_7537_cov_11_1706 cat_2 VIRSorter_NODE_2982_length_1113_cov_2_02703 cat_2 VIRSorter_NODE_150_length_2967_cov_3_60415 cat_2


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_568_length_1984_cov_4_76403 cat_2 VIRSorter_NODE_13_length_17922_cov_52_6305 cat_1 VIRSorter_NODE_433_length_2253_cov_3_42233 cat_2 VIRSorter_NODE_335_length_2021_cov_4_10391_GC021842_GC021842 cat_2 VIRSorter_NODE_138_length_3112_cov_4_00791 cat_2 VIRSorter_NODE_1458_length_1041_cov_2_11722_GC021830_GC021830


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_332_length_2175_cov_10_2507 cat_2 VIRSorter_NODE_1147_length_1321_cov_3_40756 cat_1 VIRSorter_NODE_100_length_4424_cov_7_35335 cat_2 VIRSorter_NODE_1703_length_1463_cov_2_22872 cat_2 VIRSorter_NODE_366_length_3576_cov_8_32009_GC021836_GC021836 cat_2 VIRSorter_NODE_725_length_1855_cov_10_6147 cat_2 VIRSorter_NODE_1238_length_1327_cov_2_0664 cat_2 VIRSorter_NODE_672_length_1295_cov_4_3514 cat_2 VIRSorter_NODE_79_length_6354_cov_62_2409 cat_2 VIRSorter_NODE_78_length_6260_cov_45_9512 cat_2


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_85_length_6320_cov_501_915 circular cat_2 VIRSorter_NODE_163_length_3745_cov_46_9332 cat_2 VIRSorter_NODE_116_length_6700_cov_102_421 circular cat_2


id: cord-255137-utg8k7qs
type: DNA
entity:
  VIRSorter_NODE_127_length_6304_cov_169_211 circular cat_1 VIRSorter_NODE_20_length_6493_cov_22_3178 circular cat_1 Microviridae Bog1249_12 VIRSorter_NODE_30_length_6450_cov_44_4565 circular cat_1 VIRSorter_NODE_109_length_4750_cov_17_446 cat_1 VIRSorter_NODE_1045_length_1845_cov_5_55713 cat_2 VIRSorter_NODE_108_length_8316_cov_472_248 cat_2 VIRSorter_NODE_64_length_5899_cov_14_19 cat_2 VIRSorter_NODE_487_length_1735_cov_5_00362_GC021842_GC021842 cat_2 Synechococcus phage S CBS1 VIRSorter_NODE_146_length_2708_cov_2_46446_GC021842_GC021842 cat_1 VIRSorter_NODE_52_length_6051_cov_9_17124 cat_2 VIRSorter_NODE_93_length_3875_cov_7_44392 cat_2 VIRSorter_NODE_25_length_9400_cov_16_2758 cat_2 VIRSorter_NODE_113_length_5573_cov_11_161 cat_2 VIRSorter_NODE_367_length_1788_cov_5_45763 cat_1 VIRSorter_NODE_536_length_1612_cov_4_77329 cat_2 VIRSorter_NODE_79_length_6005_cov_26_2043 cat_1 VIRSorter_NODE_48_length_9440_cov_6_63527 cat_1 VIRSorter_NODE_323_length_1422_cov_4_3658 cat_2 VIRSorter_NODE_129_length_3930_cov_23_5902 cat_2 VIRSorter_NODE_560_length_1433_cov_2_40929 cat_2 VIRSorter_NODE_141_length_3439_cov_8_81707 cat_2 VIRSorter_NODE_743_length_1379_cov_4_01382 cat_2 VIRSorter_NODE_976_length_1608_cov_2_55781 cat_2 VIRSorter_NODE_239_length_3424_cov_8_63012 cat_2 VIRSorter_NODE_51_length_4072_cov_6_41852_GC021842_GC021842 cat_2 VIRSorter_NODE_337_length_2689_cov_3_29939 cat_2 VIRSorter_NODE_730_length_1731_cov_6_55562 cat_1 VIRSorter_NODE_659_length_2336_cov_3_83267 cat_2 VIRSorter_NODE_1984_length_1222_cov_4_24629 cat_2 VIRSorter_NODE_883_length_1252_cov_3_38638 cat_2 VIRSorter_NODE_71_length_4503_cov_55_2632_ID_1234741 cat_2 Synechococcus phage S RIP1 VIRSorter_NODE_279_length_5367_cov_4_5949 cat_2 VIRSorter_NODE_86_length_5830_cov_19_66 cat_2 VIRSorter_NODE_31_length_7440_cov_34_4581 cat_2 VIRSorter_NODE_955_length_2525_cov_5_13235


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_185_length_4953_cov_6_15402 cat_1 VIRSorter_NODE_1708_length_1576_cov_4_20547 cat_2 VIRSorter_NODE_44_length_7557_cov_10_863 cat_2 VIRSorter_NODE_233_length_4482_cov_10_1639 cat_2 Pseudomonas phage AF VIRSorter_NODE_552_length_2485_cov_4_35756 cat_2 VIRSorter_NODE_192_length_3929_cov_3_8676 cat_1 VIRSorter_NODE_322_length_4472_cov_38_5126_GC021836_GC021836 cat_1 VIRSorter_NODE_538_length_2956_cov_5_02813 cat_1 VIRSorter_NODE_992_length_1573_cov_4_92848 cat_2 VIRSorter_NODE_16_length_23516_cov_138_53 cat_2 VIRSorter_NODE_151_length_1878_cov_116_108_ID_301_GC022959_GC022959 cat_1 VIRSorter_NODE_85_length_8370_cov_15_7844 cat_1 VIRSorter_NODE_15_length_11161_cov_176_621_GC021830_GC021830 cat_1 VIRSorter_NODE_2781_length_1390_cov_3_66794 cat_1 VIRSorter_NODE_1540_length_1662_cov_4_40252 cat_2 VIRSorter_NODE_14_length_17500_cov_14_0744 cat_2 VIRSorter_NODE_300_length_4134_cov_17_8536 cat_2 VIRSorter_NODE_6_length_27203_cov_21_9593 cat_2 Enterobacter phage


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_29_length_18268_cov_15_4076 cat_1 VIRSorter_NODE_110_length_5017_cov_16_0623 cat_1 Cyanophage NATL1A


id: cord-255137-utg8k7qs
type: CELL_LINE
entity:
  VIRSorter_NODE_361_length_3416_cov_6_31087 cat_1 VIRSorter_NODE_91_length_5972_cov_36_3963 cat_2 VIRSorter_NODE_376_length_1948_cov_3_65526 cat_2 Synechococcus phage S CBS3 VIRSorter_NODE_48_length_6491_cov_22_8788 cat_2 VIRSorter_NODE_116_length_5103_cov_33_1303 cat_2 VIRSorter_NODE_28_length_11201_cov_16_625 cat_2 Pseudomonas phage phiPSA2 VIRSorter_NODE_253_length_2462_cov_8_22893 cat_2 VIRSorter_NODE_810_length_1414_cov_2_10995_GC021842_GC021842 cat_1 VIRSorter_NODE_285_length_4031_cov_5_88012 cat_2 VIRSorter_NODE_245_length_3176_cov_5_55082 cat_2 VIRSorter_NODE_11_length_22035_cov_75_4007 cat_2 Xanthomonas phage Xp15 VIRSorter_NODE_399_length_2511_cov_12_2247 cat_2 VIRSorter_NODE_51_length_6198_cov_78_8288_ID_1234693 cat_1 VIRSorter_NODE_1872_length_1092_cov_1_13005 cat_2 VIRSorter_NODE_1511_length_1484_cov_3_12722 cat_2 VIRSorter_NODE_1195_length_1353_cov_8_8895 cat_2 VIRSorter_NODE_69_length_7221_cov_10_606 cat_2 VIRSorter_NODE_555_length_1364_cov_3_66667_GC021836_GC021836 cat_2 VIRSorter_NODE_3_length_41166_cov_1412_67 circular cat_2 VIRSorter_NODE_23_length_13188_cov_34_6875 cat_1 VIRSorter_NODE_9_length_34390_cov_51_9275 cat_2 VIRSorter_NODE_20_length_21130_cov_32_3079 cat_2 VIRSorter_NODE_10_length_37636_cov_94_1194 cat_2 VIRSorter_NODE_253_length_5676_cov_8_48509 cat_1 VIRSorter_NODE_174_length_3625_cov_24_6435 cat_2 VIRSorter_NODE_63_length_10962_cov_10_2398 cat_1 VIRSorter_NODE_4_length_95574_cov_53_2034 cat_2 VIRSorter_NODE_44_length_12771_cov_25_968 cat_2 VIRSorter_NODE_93_length_5511_cov_39_8675 cat_1 VIRSorter_NODE_1_length_63229_cov_49_3797 cat_2 VIRSorter_NODE_1_length_62610_cov_351_397 cat_2 VIRSorter_NODE_428_length_1474_cov_31_388 cat_2 VIRSorter_NODE_10_length_8122_cov_44_0481_GC021842_GC021842 cat_2 VIRSorter_NODE_84_length_7309_cov_13_3547 cat_2 VIRSorter_NODE_113_length_3110_cov_6_34454 cat_1 VIRSorter_NODE_156_length_3846_cov_90_3208 cat_2 VIRSorter_NODE_3_length_52558_cov_119_096 cat_2 VIRSorter_NODE_58_length_2924_cov_7_11907 cat_1 VIRSorter_NODE_136_length_1738_cov_8_4401 cat_2 VIRSorter_NODE_119_length_3091_cov_3_65196 cat_2 VIRSorter_NODE_71_length_5867_cov_6_41969 cat_2 VIRSorter_NODE_3_length_41933_cov_233_011 cat_2 VIRSorter_NODE_258_length_3503_cov_8_13689 cat_2 VIRSorter_NODE_321_length_1425_cov_3_60831 cat_1 VIRSorter_NODE_3_length_47484_cov_53_1945 cat_2 VIRSorter_NODE_6_length_18914_cov_22_0195 cat_2 VIRSorter_NODE_58_length_6232_cov_20_7313 cat_2 family


id: cord-255137-utg8k7qs
type: PROTEIN
entity:
  JX857869_HumanAstV VA4 human Nepal s5363 HQ916317_BovineAstV B76 2 HK FJ890352_Sea_lionAstV2 Z25771_HumanAstV Newcastle HQ916313_BovineAstV B18 HK HQ916317_BovineAstV B76 2


id: cord-255137-utg8k7qs
type: GGP
entity:
  cat_1 VIRSorter_NODE_285_length_4031_cov_5_88012 cat_2 VIRSorter_NODE_245_length_3176_cov_5_55082 cat_2 VIRSorter_NODE_11_length_22035_cov_75_4007 cat_2 Xanthomonas phage Xp15 VIRSorter_NODE_399_length_2511_cov_12_2247


id: cord-255137-utg8k7qs
type: PERSON
entity:
  BPP1 VIRSorter_NODE_27_length_13648_cov_10_3894 cat_1 VIRSorter_NODE_16_length_5962_cov_37_6794_ID_31_GC022959_GC022959


id: cord-255137-utg8k7qs
type: CHEMICAL
entity:
  Bacteroidaceae Bifidobacteriaceae Enterobacteriaceae Enterococcaceae Erysipelotrichaceae Eubacteriaceae Lactobacillaceae Odoribacteraceae Streptococcaceae


id: cord-255137-utg8k7qs
type: CHEMICAL
entity:
  VIRSorter_NODE_193_length_2388_cov_2_87797 cat_2 VIRSorter_NODE_25_length_14198_cov_12_3353 cat_2 VIRSorter_NODE_83_length_6779_cov_23_1462


id: cord-255137-utg8k7qs
type: CHEMICAL
entity:
  VIRSorter_NODE_6_length_39977_cov_34_3534 cat_2 VIRSorter_NODE_145_length_6050_cov_14_9503 cat_2 VIRSorter_NODE_3_length_55511_cov_174_071 cat_2


id: cord-255137-utg8k7qs
type: CHEMICAL
entity:
  VIRSorter_NODE_659_length_2336_cov_3_83267 cat_2 VIRSorter_NODE_1984_length_1222_cov_4_24629 cat_2 VIRSorter_NODE_883_length_1252_cov_3_38638 cat_2 VIRSorter_NODE_71_length_4503_cov_55_2632_ID_1234741 cat_2 Synechococcus phage S RIP1


id: cord-287748-co9j3uig
type: CELL_LINE
entity:
  mammalian cell lines Madin Darby canine kidney MDCK African green monkey VeroE6 human A549 Madin Darby bovine kidney MDBK


id: cord-281956-obwtd33y
type: ORG
entity:
  the European Convention for the Protection of Vertebrate Animals Used for Experimental and Other Scientific


id: cord-277306-r8jki3x4
type: ORG
entity:
  the University of Colorado School of Medicine Cancer Center DNA Sequencing and Analysis Core Samples


id: cord-277306-r8jki3x4
type: WORK_OF_ART
entity:
  Guidelines of the American Society of Mammalogists for the use of wild mammals in research Distribution and Ecology of Bats of


id: cord-289584-rbp7p8s9
type: PROTEIN
entity:
  PDCoV CHJXNI2 2015 KR131621 1 Porcine coronavirus HKU15 strain HKU15 44 NC016990 Bulbul coronavirus HKU11 796


id: cord-342124-jdv17u86
type: GGP
entity:
  biológica y cultural Node centrality in weighted networks Generalizing degree and shortest paths Ecological dynamics of emerging bat virus spillover R A


id: cord-342124-jdv17u86
type: DISEASE
entity:
  Sin Nombre virus Puumala virus Crimean Congo hemorrhagic fever virus Kyasanur forest virus tick borne encephalitis virus Lassa fever virus and Venezuelan equine encephalitis virus


id: cord-272250-asuxx1ln
type: ORG
entity:
  Amazon Human Rabies Prevention 2008 Recommendations of the Advisory Committee for Immunization Practices Nipah


id: cord-102977-yci9kq6x
type: PROTEIN
entity:
  antibodies F4 80 Monoclonal Antibody 1 100 MF48000 Thermo Fisher 398 Scientific Anti IL 6 antibody 1 100


id: cord-017785-zwnkrs23
type: DNA
entity:
  nuclear factor kB NF kB family member REL IFNAR1 Toll like receptor 7 TLR7 IFN stimulated gene 15 ISG15 interleukin 18 IL 18


id: cord-283756-ycjzitlk
type: DISEASE
entity:
  henipaviruses in fruit juice lychee pawpaw and mango over three to four days although titres were still detectable after three days There were also large variations


id: cord-284015-vvtv492b
type: DNA
entity:
  14 mammals cat dog horse cow hedgehog human macaque mouse rat Black flying fox Little brown bat Brandt s bat David s myotis and Large flying fox Supplementary Table S2


id: cord-284015-vvtv492b
type: CL
entity:
  stem and crown megabat branches The species tree shown in Fig 1 was used as a guide tree in the analysis Likelihood ratio tests and inspections of the P value were used to compare likelihoods between two models i that assumed the megabat lineages as foreground branches and ii that assumed the dN dS


id: cord-295433-olmein3q
type: DISEASE
entity:
  coronaviruses in Cardioderma cor Ediolon helvum Epomophorus labiatuc Hipposideros sp Miniopterus minor Otomops martiensseni Rhinolophus hildebrandtii Rhinolophus sp


id: cord-338055-2d6n4cve
type: CHEMICAL
entity:
  N terminal hydrophobic signal peptide 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 aa and an ORF8 chain 16 121 aa 16 17 The functional motif VLVVL


id: cord-347532-n51qv9pp
type: DNA
entity:
  Wacharapluesadee Supaporn Sintunawa Chirapol Kaewpom Thongchai Khongnomnan Kritsada Olival Kevin J Epstein Jonathan H Rodpan Apaporn Sangsri Paiboon Intarut Nirun Chindamporn Ariya Suksawa Kanyarat Hemachudha Thiravat title Group C Betacoronavirus


id: cord-289555-1z4vbldd
type: WORK_OF_ART
entity:
  Diseases and Causes of Death in European Bats Dynamics in Disease Susceptibility and Infection Rates


id: cord-289555-1z4vbldd
type: DISEASE
entity:
  lung liver heart kidney adrenal gland spleen intestine pancreas brain tongue larynx salivary gland and pectoral muscle


id: cord-324295-9c1zxjng
type: PROTEIN
entity:
  recombinant viral glycoprotein NIH Rabies Vaccine Drugs and Lactation Database LactMed Ecoepidemiological and Social Factors


id: cord-308614-gsgntf4c
type: CELL_LINE
entity:
  median brachial vein cranial vena cava jugular vein orbital sinus and heart 2 3 4 Venipuncture of the cephalic and the saphenous interfemoral veins


id: cord-308614-gsgntf4c
type: DISEASE
entity:
  brachial vein cranial vena cava jugular vein orbital sinus and heart 2 3 4 Venipuncture of the cephalic


id: cord-343206-9tqivs5f
type: FAC
entity:
  Satellites Uncover 5 Surprising Hotspots for Tree Cover Loss World Resources Institute Identification


id: cord-315972-5g2hnk1x
type: SO
entity:
  forward 5 ATGGGITGGGAY TATCCWAARTGTG 3 1st round reverse 5 AATTAT ARCAIACAACISYRTCRTCA 3 2nd round reverse 5 CTAGTICCACCIGGYTTWANRTA 3 For the pan bat coronavirus


id: cord-310734-6v7oru2l
type: WORK_OF_ART
entity:
  A Preliminary Study of the Virome of the South American Free Tailed Bats Tadarida brasiliensis and Identification of Two Novel Mammalian Viruses date 2020 04 09


id: cord-310734-6v7oru2l
type: WORK_OF_ART
entity:
  Metagenomic Analysis of Viruses from Bat Fecal Samples Reveals Many Novel Viruses in Insectivorous Bats in China Evaluation


id: cord-310734-6v7oru2l
type: CHEMICAL
entity:
  3R 5 atgcccgggaa tatggatgga 3 TbraPV1 4F 5 ggcctgcaagaccacctac 3 and TbraPV1 4R 5 gggggcatctgacctgtta 3


id: cord-308932-pp8etmwq
type: GGP
entity:
  bat Toll like receptors 3 7 and 9 Cloning expression and antiviral activity of IFNc from the Australian fruit bat Pteropus alecto


id: cord-310061-nro623aa
type: PROTEIN
entity:
  cytochrome oxidase subunit 1 genes CO1 35 One PCR amplicon was selected for sequencing and compared to reference sequences


id: cord-310061-nro623aa
type: GGP
entity:
  alpha coronaviruses PREDICT_CoV 35 47 82 and 90 and three betacoronavirues PREDICT CoV 92 93 and 96 Of these the alphacoronavirus PREDICT_CoV 35


id: cord-310061-nro623aa
type: ORG
entity:
  the Ministry of Agriculture Livestock and Irrigation MOALI Ministry of Natural Resources and Environmental Conservation MONREC


id: cord-338400-30vl2hks
type: PROTEIN
entity:
  bilirubin alkaline phosphatase alanine transferase aspartate aminotransferase gamma glutamyltransferase


id: cord-338400-30vl2hks
type: PROTEIN
entity:
  helicase C pfam 00271 NS4A pfam 01006 NS4B pfam 01001 NS5A domain 1a zinc finger pfam 08300 domain 1b pfam 08301


id: cord-329617-gzivtsho
type: ORG
entity:
  the Guide for the Care and Use of Laboratory Animals Committee for the Update of the Guide for the Care and Use of Laboratory Animals


id: cord-293946-4bquxdqa
type: GGP
entity:
  geoBoundaries v 3 0 0 https www geoboundaries org 34 and Open Development Mekong https vietnam opendevelopmentmekong net All analyses were done using R version 3 5 0


id: cord-327534-f2wvh6la
type: DNA
entity:
  ENSP00000380697 Homo sapiens human ENSMUSP00000095565 Mus musculus mouse ENSECAP00000007698 Equus caballus horse ENSSSCP00000013664 Sus scrofa


id: cord-327534-f2wvh6la
type: DISEASE
entity:
  brain kidney liver lung lymph nodes spleen heart small intestine wing salivary gland thymus and testis


id: cord-352361-jh31omg2
type: DNA
entity:
  genus Orthobornavirus Mammalian 1 orthobornavirus Mammalian 2 orthobornavirus Passeriform 1 orthobornavirus Passeriform 2 orthobornavirus Psittaciform 1 orthobornavirus Psittaciform 2 orthobornavirus and Waterbird 1


id: cord-291965-9r9ll83m
type: GGP
entity:
  CoVs 7 25 26 36 37 38 We have confirmed all tree topologies using alternative methods of phylogenetic inference


id: cord-313472-skcaw9ls
type: DNA
entity:
  Nipah virus 13 14 the Hendra virus 15 Ebola 16 lyssaviruses 17 and severe acute respiratory syndrome coronavirus SARS CoV 2 18 19


id: cord-313472-skcaw9ls
type: ORG
entity:
  The Department of National Park Wildlife and Plant Conservation Ministry of Natural Resources and Environment


id: cord-338586-rkrkofri
type: TAXON
entity:
  Rhabdoviridae Orthomyxoviridae Paramyxoviridae Coronaviridae Togaviridae Flaviviridae Bunyaviridae Reoviridae Arenaviridae Herpesviridae Picornaviridae


id: cord-265357-3f0xph0y
type: DNA
entity:
  G31 Mluc 34 D15 H19 H23 H29 35 Mnatt 1 Mnatt 2 36 Mschreib3 37 Mnatt 8 Mnatt 11 38 FV5AP 39 and GZBYR 5 TCCTTGTCACTATAAGCTCAGTGG 3 forward 5 CCAGGCAATAGTCTCCTAGCAC 3


id: cord-265357-3f0xph0y
type: DNA
entity:
  Schreibers long fingered bat Miniopterus schreibersii Chiroptera Vespertilionidae Isolation and characterization of eight polymorphic microsatellite loci


id: cord-354738-4rxradwz
type: TAXON
entity:
  bat species Pipistrellus pipistrellus Pipistrellus nathusii Pipistrellus kuhlii and Nyctalus noctula


id: cord-317244-4su5on6s
type: PROTEIN
entity:
  Nariva virus NarPV 2 Mossman virus MosPV 3 Beilong virus BeiPV 4 J virus JPV 5 6 Tupaia paramyxovirus TupPV 7


id: cord-317244-4su5on6s
type: DISEASE
entity:
  Flaviviruses Alphaviruses polyomaviruses Orthopoxviruses Parapoxviruses Influenza viruses Lyssaviruses and Rhabdoviridae family


id: cord-294698-mtfrbn87
type: DISEASE
entity:
  acute respiratory syndrome coronavirus SARS CoV Middle East respiratory syndrome coronavirus MERS CoV Nipah


id: cord-294698-mtfrbn87
type: DISEASE
entity:
  acute respiratory syndrome coronavirus SARS CoV Middle East respiratory syndrome coronavirus MERS CoV Nipah virus Hendra virus and Ebola virus


id: cord-304481-yqc8r3ll
type: WORK_OF_ART
entity:
  A Language and Environment for Statistical Computing R Foundation for Statistical Computing Phylogenomic


id: cord-350286-n7ylgqfu
type: GGP
entity:
  bioRxiv DOI 10 1101 2020 03 13 990598 sha 7b1d3cd2210cdb4bb41a1af294cf02bd04f58525 doc_id 350286 cord_uid n7ylgqfu Recently emerged coronavirus designated


id: cord-350286-n7ylgqfu
type: GGP
entity:
  Human SARS CoV 72 99 Graphs in Figures 7A 7B and 7C depict the propensity for disorder in ORF3a proteins


id: cord-350286-n7ylgqfu
type: ORG
entity:
  Noncanonical Transcription Initiation Signals of Severe Acute Respiratory Syndrome Coronavirus Ultrastructure and Origin of Membrane Vesicles Associated


id: cord-350286-n7ylgqfu
type: ORG
entity:
  the Severe Acute Respiratory Syndrome Coronavirus Are Required for Efficient Assembly Trafficking and Release of Virus Like Particles Multiple Nucleic Acid Binding Sites


id: cord-350286-n7ylgqfu
type: ORG
entity:
  Animal Severe Acute Respiratory Syndrome Coronaviruses Disrupts the Functional Expression of Open Reading Frame 8


id: cord-352563-yb446bap
type: CELL_LINE
entity:
  293 human embryo kidney cells A549 human lung carcinoma cells Huh7 human hepatoma cells HT29 human colon cancer cells


id: cord-352563-yb446bap
type: ORG
entity:
  the National Science and Technology Major Project of the Ministry of Science and Technology of China


id: cord-334628-axon4jdc
type: DISEASE
entity:
  coronavirus in Korean bat samples was 2 7 overall The prevalence by sample type was 5 4 13 332 for oral swabs 1 8 1 57 for carcasses 1 6 4 245


id: cord-355075-ieb35upi
type: PROTEIN
entity:
  ISGs myxovirus resistance Mx GTPases Protein kinase R PKR 2 5 oligoadenylate synthetases OAS ribonuclease L RNaseL


id: cord-355075-ieb35upi
type: ORG
entity:
  Chicken Is Characterized by Massive Expansion and Diversification of Immunoglobulin Like Loci The Chicken Leukocyte Receptor


# bib

id: cord-001455-n7quwr4s
author: Rapin, Noreen
date: 2014-11-12
txt: ./txt/cord-001455-n7quwr4s.txt
cache: ./cache/cord-001455-n7quwr4s.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229191/
doi: 10.1371/journal.pone.0112285
summary:
  title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans Using tissue samples collected at the termination of an experiment to explore the pathogenesis of White Nose Syndrome in Little Brown Bats, we determined if hibernating bats infected with the fungus Pseudogymnoascus destructans could respond to infection by activating genes responsible for innate immune and stress responses. We found that bats responded to infection with a significant increase in lungs of transcripts for Cathelicidin (an anti-microbial peptide) as well as the immune modulators tumor necrosis factor alpha and interleukins 10 and 23. We used samples collected during the experiment to address the question: Can hibernating bats respond to infection by activating genes responsible for innate immune and stress responses? We determined levels of transcripts for several immune and stress response genes (Table 1) in lungs from infected and control bats.

title:
  Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans

abstract:
  Recently bats have been associated with the emergence of diseases, both as reservoirs for several new viral diseases in humans and other animals and, in the northern Americas, as hosts for a devastating fungal disease that threatens to drive several bat species to regional extinction. However, despite these catastrophic events little Information is available on bat defences or how they interact with their pathogens. Even less is known about the response of bats to infection during torpor or long-term hibernation. Using tissue samples collected at the termination of an experiment to explore the pathogenesis of White Nose Syndrome in Little Brown Bats, we determined if hibernating bats infected with the fungus Pseudogymnoascus destructans could respond to infection by activating genes responsible for innate immune and stress responses. Lesions due to fungal infection and, in some cases, secondary bacterial infections, were restricted to the skin. However, we were unable to obtain sufficient amounts of RNA from these sites. We therefore examined lungs for response at an epithelial surface not linked to the primary site of infection. We found that bats responded to infection with a significant increase in lungs of transcripts for Cathelicidin (an anti-microbial peptide) as well as the immune modulators tumor necrosis factor alpha and interleukins 10 and 23. In conclusion, hibernating bats can respond to experimental P. destructans infection by activating expression of innate immune response genes.


id: cord-003166-k3jxvzfi
author: Noh, Ji Yeong
date: 2018-08-22
txt: ./txt/cord-003166-k3jxvzfi.txt
cache: ./cache/cord-003166-k3jxvzfi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105681/
doi: 10.1038/s41598-018-30319-7
summary:
  Even though the HN amino acids sequences were similar to those from viruses in the proposed genera Shaanvirus, it was also related to that of Sendai virus and human parainfluenza virus 1, which belong to a different genus, Respirovirus showing (Table 1) . In addition, among three pooled sera (two mouse sera each) against human parainfluenza virus 1 (KBPV-VR-44), one pooled serum was cross-reactive to the bat paramyxovirus B16-40 with 40 as the end-point titer for the fluorescent signal ( Table 2 , Fig. 4 ). Notably, even though the HN amino acids sequences were similar to those from viruses in the proposed genera Shaanvirus, it was also related to that of Sendai virus and human parainfluenza virus 1, which belong to a different genus, Respirovirus (Table 1) . In fact, in this study, when mouse antisera were made and tested against bat paramyxovirus B16-40 and human parainfluenza virus 1 (KBPV-VR-44), the two viruses were partially cross-reactive to each other in an indirect immunofluorescence assay.

title:
  Isolation and characterization of novel bat paramyxovirus B16-40 potentially belonging to the proposed genus Shaanvirus

abstract:
  The bat paramyxovirus B16-40 was first isolated in Korea in this study. Using the isolated virus, we could obtain not only genomic information, but also several biological characteristics of the virus. In the phylogenetic analysis, the virus was found to belong to the recently proposed genus Shaanvirus. Through sequence analyses and in vitro testing, the isolated virus was also found to have haemagglutinin-neuraminidase (HN) protein as one of the structural proteins. When mouse antiserum was generated against the isolated virus and tested, it was cross-reactive to human parainfluenza virus 1 in an indirect immunofluorescence assay but could not cross-neutralize human parainfluenza virus 1. In addition, the bat paramyxovirus B16-40 was not infectious in the mouse model. Collectively, this study provided basic information on further classification of the bat paramyxovirus B16-40 and related viruses in the proposed genus Shaanvirus.


id: cord-003232-nquw7qga
title: Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection
author: Kuchipudi, Suresh V.
date: 2018-08-06
txt: ./txt/cord-003232-nquw7qga.txt
cache: ./cache/cord-003232-nquw7qga.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6165133/
doi: 10.3390/vetsci5030071
summary:
  This review examines the recent discovery of novel influenza viruses in bats and cattle, the evolving complexity of influenza virus host range including the ability to cross species barriers and geographic boundaries, and implications to animal and human health. In addition, we discussed the growing complexity of influenza virus-host interactions and highlighted the key research questions that need to be answered for a better understanding of the emergence of pandemic influenza viruses. Ability to infect a wide range hosts is a key contributing factor to the complex and seemingly expanding genetic diversity of IAVs. It is now well established that IAVs infect domestic pets such as dogs and cats, adding to the list of host species that could potentially expose humans to influenza viruses. Although influenza viruses infect humans and a wide range of animals and birds, cattle were never considered to be susceptible to influenza virus infection.

abstract:
  Influenza viruses are among the major infectious disease threats of animal and human health. This review examines the recent discovery of novel influenza viruses in bats and cattle, the evolving complexity of influenza virus host range including the ability to cross species barriers and geographic boundaries, and implications to animal and human health.


id: cord-003482-f1uvohf0
author: Malmlov, Ashley
date: 2019-02-04
txt: ./txt/cord-003482-f1uvohf0.txt
cache: ./cache/cord-003482-f1uvohf0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382173/
doi: 10.1371/journal.pntd.0007071
summary:
  Quantitative probe-based reverse transcription PCR (qRT-PCR) was performed on seruminoculated Vero cell supernatants, serum, brain, lung, liver, spleen, kidney, urinary bladder, prostate and testes from bats from both studies. Brain and testicular tissues stained with both goat polyclonal goat anti-Iba1 (green) and monoclonal 4G-2 flavivirus E specific antibodies (red) showed co-localization (yellow) of ZIKV antigen in cytoplasm of activated microglial cells with their characteristic morphology in the cerebral cortex of infected bats 10 dpi in the time course study and 28 day dpi in the pilot study (Fig 9) . Two bat infection experiments were conducted in this investigation; 1) a pilot study to determine susceptibility of Jamaican fruit bats to ZIKV infection, and 2) a time course study to better understand pathophysiology and chronology of events pertaining to the dynamics of viremia, viral tropism, replication and shedding of the virus in a New World bat species.

title:
  Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells

abstract:
  The emergence of Zika virus (ZIKV) in the New World has led to more than 200,000 human infections. Perinatal infection can cause severe neurological complications, including fetal and neonatal microcephaly, and in adults there is an association with Guillain-Barré syndrome (GBS). ZIKV is transmitted to humans by Aedes sp. mosquitoes, yet little is known about its enzootic cycle in which transmission is thought to occur between arboreal Aedes sp. mosquitos and non-human primates. In the 1950s and ‘60s, several bat species were shown to be naturally and experimentally susceptible to ZIKV with acute viremia and seroconversion, and some developed neurological disease with viral antigen detected in the brain. Because of ZIKV emergence in the Americas, we sought to determine susceptibility of Jamaican fruit bats (Artibeus jamaicensis), one of the most common bats in the New World. Bats were inoculated with ZIKV PRVABC59 but did not show signs of disease. Bats held to 28 days post-inoculation (PI) had detectable antibody by ELISA and viral RNA was detected by qRT-PCR in the brain, saliva and urine in some of the bats. Immunoreactivity using polyclonal anti-ZIKV antibody was detected in testes, brain, lung and salivary glands plus scrotal skin. Tropism for mononuclear cells, including macrophages/microglia and fibroblasts, was seen in the aforementioned organs in addition to testicular Leydig cells. The virus likely localized to the brain via infection of Iba1(+) macrophage/microglial cells. Jamaican fruit bats, therefore, may be a useful animal model for the study of ZIKV infection. This work also raises the possibility that bats may have a role in Zika virus ecology in endemic regions, and that ZIKV may pose a wildlife disease threat to bat populations.


id: cord-003757-uwbpbai7
author: Chionh, Yok Teng
date: 2019-06-22
txt: ./txt/cord-003757-uwbpbai7.txt
cache: ./cache/cord-003757-uwbpbai7.txt
extension: .txt
mime: text/plain
url: https://link.springer.com/content/pdf/10.1007/s12192-019-01013-y.pdf
doi: 10.1007/s12192-019-01013-y
summary:
  Heat shock protein (HSP), highly conserved master regulators of cell stress, expression was examined across tissues and various cell lines in bats. Here, we show that bats have elevated expression of heat shock proteins (HSPs) in various tissue and cell lines from two species, comparative sequence analysis of HSPs from ten bat species and that increased HSP expression in vitro confers survival of cells during prolonged heat stress. For kidney, we found that PaKiT03 (bat) cells expressed significantly higher amounts of HSP70 and HSP90A/B both at the mRNA (Fig. 2b-d) and protein levels (Fig. 2e) at 37°C compared to the MDCK (dog) and BHK (hamster) cells under normal conditions. The basal expression level of several HSP genes is genetically imprinted in vivo in live animal-derived tissues from two species of bat, with cultured cell lines displaying the same high expression.

title:
  High basal heat-shock protein expression in bats confers resistance to cellular heat/oxidative stress

abstract:
  Bats, unique among mammals with powered flight, have many species with the longest size-proportionate lifespan of all mammals. Evolutionary adaptations would have been required to survive the elevated body temperatures during flight. Heat shock protein (HSP), highly conserved master regulators of cell stress, expression was examined across tissues and various cell lines in bats. Basal expression level of major HSPs (HSP70 and HSP90) is significantly higher in two different bat species compared to other mammals. This HSP expression could be a bat-unique, key factor to modulate cellular stress and death. Consequently, bat cells survive prolonged heat treatment, along with other stress stimuli, in a HSP-dependent manner, whereas other mammalian cells succumbed. This suggests HSP expression in bats could be an important adaption to intrinsic metabolic stresses like flight and therefore an important model to study stress resilience and longevity in general. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12192-019-01013-y) contains supplementary material, which is available to authorized users.


id: cord-003775-1axsebya
title: Hypsugopoxvirus: A Novel Poxvirus Isolated from Hypsugo savii in Italy
author: Lelli, Davide
date: 2019-06-19
txt: ./txt/cord-003775-1axsebya.txt
cache: ./cache/cord-003775-1axsebya.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6631891/
doi: 10.3390/v11060568
summary:
  Herein, we report the isolation, nearly complete genome sequencing, and annotation of a novel poxvirus detected from an insectivorous bat (Hypsugo savii) in Northern Italy. In this study, we report the isolation, nearly complete genomic sequencing, and annotation of a novel poxvirus detected from an insectivorous bat (Hypsugo savii) in Northern Italy. Phylogenetic analyses suggest that HYPV belongs to the Chordopoxvirinae subfamily, revealing the highest similarity (85%) with Eptesipoxvirus (EPTV) detected from the microbat Eptesicus fuscus in WA, USA in 2011, which is associated with bat necrosuppurative osteomyelitis in multiple joints. For the nearly complete viral genome sequencing, BLAST analysis revealed the highest nucleotide identity (85%) to the Eptesipoxvirus (EPTV) strain "Washington", a member of the Chordopoxvirinae subfamily identified in microbats in the USA ( Table 2 ). To conclude, a new poxvirus, HYPV, was detected in bats in Europe and its viral ecology and disease associations should be investigated further.

abstract:
  Interest in bat-related viruses has increased considerably during the last decade, leading to the discovery of a rising number of new viruses in several bat species. Poxviridae are a large, diverse family of DNA viruses that can infect a wide range of vertebrates and invertebrates. To date, only a few documented detections of poxviruses have been described in bat populations on three different continents (America, Africa, and Australia). These viruses are phylogenetically dissimilar and have diverse clinical impacts on their hosts. Herein, we report the isolation, nearly complete genome sequencing, and annotation of a novel poxvirus detected from an insectivorous bat (Hypsugo savii) in Northern Italy. The virus is tentatively named Hypsugopoxvirus (HYPV) after the bat species from which it was isolated. The nearly complete genome size is 166,600 nt and it encodes 161 genes. Genome analyses suggest that HYPV belongs to the Chordopoxvirinae subfamily, with the highest nucleotide identity (85%) to Eptesipoxvirus (EPTV) detected from a microbat Eptesicus fuscus in WA, USA, in 2011. To date, HYPV represents the first poxvirus detected in bats in Europe; thus, its viral ecology and disease associations should be investigated further.


id: cord-004502-3mkv3bal
author: Wei, Gang
date: 2020-03-16
txt: ./txt/cord-004502-3mkv3bal.txt
cache: ./cache/cord-004502-3mkv3bal.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7076951/
doi: 10.1186/s12986-020-00440-4
summary:
  Moreover, we revealed that indirubin treatment increased BAT activity by promoting thermogenesis and mitochondrial biogenesis in BAT and induced browning of subcutaneous inguinal white adipose tissue (sWAT) of mice under HFD. Correspondly, a pharmacological approach to increase UCP1 expression and activates of BAT thermogenesis and (or) recruits brown-like brite/beige cells in WAT may be a safer avenue to enhance wholebody energy expenditure, one complementary and alternative medicine for anti-obesity therapy [32, 33] . Our results indicate that as an effective BAT (as well as beige cell) activator, indirubin may have a protective effect on the prevention and treatment of obesity and related diseases, which involved in the up-regulation of UCP1 expression and enhancing the BAT activity and (or) inducing browning of sWAT, at least in part, via activation of PKA and p38MAPK signaling pathways.

title:
  Indirubin, a small molecular deriving from connectivity map (CMAP) screening, ameliorates obesity-induced metabolic dysfunction by enhancing brown adipose thermogenesis and white adipose browning

abstract:
  BACKGROUND: Obesity occurs when the body’s energy intake is constantly greater than its energy consumption and the pharmacological enhancing the activity of brown adipose tissue (BAT) and (or) browning of white adipose tissue (WAT) has been considered promising strategies to treat obesity. METHODS: In this study, we took a multi-pronged approach to screen UCP1 activators, including in silico predictions, in vitro assays, as well as in vivo experiments. RESULTS: Base on Connectivity MAP (CMAP) screening, we obtained multiple drugs that possess a remarkably correlating gene expression pattern to that of enhancing activity in BAT and (or) sWAT signature. Particularly, we focused on a previously unreported drug-indirubin, a compound obtained from the Indigo plant, which is now mainly used for the treatment of chronic myelogenous leukemia (CML). In the current study, our results shown that indirubin could enhance the BAT activity, as evidenced by up-regulated Ucp1 expression and enhanced mitochondrial respiratory function in vitro cellular model. Furthermore, indirubin treatment restrained high-fat diet (HFD)-induced body weight gain, improved glucose homeostasis and ameliorated hepatic steatosis which were associated with the increase of energy expenditure in the mice model. Moreover, we revealed that indirubin treatment increased BAT activity by promoting thermogenesis and mitochondrial biogenesis in BAT and induced browning of subcutaneous inguinal white adipose tissue (sWAT) of mice under HFD. Besides, our results indicated that indirubin induced UCP1 expression in brown adipocytes, at least in part, via activation of PKA and p38MAPK signaling pathways. CONCLUSIONS: Our results clearly show that as an effective BAT (as well as beige cells) activator, indirubin may have a protective effect on the prevention and treatment of obesity and its complications.


id: cord-004510-cbutpjre
author: Seetahal, Janine F. R.
date: 2020-02-05
txt: ./txt/cord-004510-cbutpjre.txt
cache: ./cache/cord-004510-cbutpjre.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077287/
doi: 10.3390/v12020178
summary:
  We aimed to determine the seroprevalence of rabies virus neutralizing antibodies (RVNA) in light of spatio-temporal and bat demographic factors to infer the extent of natural exposure to RABV in the Trinidadian bat population. RVNA titers were determined by the RABV micro-neutralization test on 383 bat samples representing 21 species, comprising 30.9% of local bat diversity, from 31 locations across the island over 5 years. We therefore sought to determine the current seroprevalence of rabies virus neutralizing antibodies (RVNA) in the Trinidadian bat population over a period of five years in order to infer the extent of natural exposure to RABVs and the spatio-temporal dynamics of RABV infection in the bat population. In Latin America and the Caribbean, the previous serological studies revealed significantly variable rates for the prevalence of rabies antibodies in bats [29] [30] [31] [39] [40] [41] [42] [43] [44] which may be attributed to differences in viral population dynamics influenced by spatio-temporal and bat demographic factors as discussed below.

title:
  The Serological Prevalence of Rabies Virus-Neutralizing Antibodies in the Bat Population on the Caribbean Island of Trinidad

abstract:
  Rabies virus (RABV) is the only lyssavirus known to be present within the Caribbean. The island of Trinidad, is richly diverse in chiropteran fauna and endemic for bat-transmitted rabies with low RABV isolation rates observed in this population. We aimed to determine the seroprevalence of rabies virus neutralizing antibodies (RVNA) in light of spatio-temporal and bat demographic factors to infer the extent of natural exposure to RABV in the Trinidadian bat population. RVNA titers were determined by the RABV micro-neutralization test on 383 bat samples representing 21 species, comprising 30.9% of local bat diversity, from 31 locations across the island over 5 years. RVNA was positively detected in 33 samples (8.6%) representing 6 bat species (mainly frugivorous) with titers ranging from 0.1 to 19 IU/mL (mean 1.66 IU/mL). The analyses based on a multivariable binomial generalised linear mixed-effects model showed that bat age and year of capture were significant predictors of seropositivity. Thus, juvenile bats were more likely to be seropositive when compared to adults (estimate 1.13; p = 0.04) which may suggest early exposure to the RABV with possible implications for viral amplification in this population. Temporal variation in rabies seropositivity, 2012–2014 versus 2015–2017 (estimate 1.07; p = 0.03) may have been related to the prevailing rabies epizootic situation. Regarding other factors investigated, RVNA was found in bats from both rural and non-rural areas, as well as in both hematophagous and non-hematophagous bat species. The most common seropositive species, Artibeus jamaicensis planirostris is ubiquitous throughout the island which may potentially facilitate human exposure. The findings of this study should be factored into public health assessments on the potential for rabies transmission by non-hematophagous bats in Trinidad.


id: cord-005012-bgo0uwob
title: Host Biology and Anthropogenic Factors Affect Hepadnavirus Infection in a Neotropical Bat
author: Hiller, Thomas
date: 2018-12-18
txt: ./txt/cord-005012-bgo0uwob.txt
cache: ./cache/cord-005012-bgo0uwob.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088011/
doi: 10.1007/s10393-018-1387-5
summary:
  We show that it is widespread and highly diversified in Peters'' tent-making bats (Uroderma bilobatum) within Panama, while local prevalence varied significantly between sample sites, ranging from 0 to 14.3%. Hepatitis B, a representative of these orthohepadnaviruses, is one of the most common and serious viral infectious diseases in humans, causing acute and chronic infections of the liver, resulting in an estimated 900,000 deaths each year (WHO Global Hepatitis Report 2017). The tent-making bat Hepatitis B virus (TBHBV), isolated from Peters'' tent-making bats (Uroderma bilobatum) in Panama, is antigenically closely related to primate HBV (Drexler et al. In fact, this close relatedness offers an exceptional possibility to study disease transmission among host bats in their natural environment, as mechanisms and restrictions might be directly adapted from well-studied host-virus interaction in humans and animals (Seeger and Mason 2000; Menne and Cote 2007; Wang et al.

abstract:
  The tent-making bat hepatitis B virus (TBHBV) is a hepadnavirus closely related to human hepatitis B virus. The ecology of TBHBV is unclear. We show that it is widespread and highly diversified in Peters’ tent-making bats (Uroderma bilobatum) within Panama, while local prevalence varied significantly between sample sites, ranging from 0 to 14.3%. Females showed significantly higher prevalence than males, and pregnant females were more often acutely infected than non-reproductive ones. The distribution of TBHBV in bats was significantly affected by forest cover, with higher infection rates in areas with lower forest cover. Our data indicate that loss of natural habitat may lead to positive feedback on the biotic factors driving infection possibility. These results underline the necessity of multidisciplinary studies for a better understanding of mechanisms in pathogen–host relationships and for predictions in disease ecology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10393-018-1387-5) contains supplementary material, which is available to authorized users.


id: cord-006502-6ajms947
title: Perivascular Adipose Tissue: the Sixth Man of the Cardiovascular System
author: Cheng, Chak Kwong
date: 2018-08-31
txt: ./txt/cord-006502-6ajms947.txt
cache: ./cache/cord-006502-6ajms947.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101924/
doi: 10.1007/s10557-018-6820-z
summary:
  PVAT does not only release PVAT-derived relaxing factors (PVRFs) to activate multiple subsets of endothelial and vascular smooth muscle potassium channels and anti-inflammatory signals in the vasculature, but it does also provide an interface for neuron-adipocyte interactions in the vascular wall to regulate arterial vascular tone. In contrast, certain PVAT (like coronary PVAT) is more beige adipose tissue-like since the expression levels of brown adipocyte-related genes, including cell deathinducing DNA fragmentation factor-α-like effector A (CIDEA), UCP-1, and carnitine palmitoyltransferase 1 B (CPT 1 B), are apparently different from those of typical BAT in studies using fat deposits collected from 129SVE mice and human [11, 12] . Interactions between vascular wall and perivascular adipose tissue reveal novel roles for adiponectin in the regulation of endothelial nitric oxide synthase function in human vessels

abstract:
  Perivascular adipose tissue (PVAT) refers to the local aggregate of adipose tissue surrounding the vascular tree, exhibiting phenotypes from white to brown and beige adipocytes. Although PVAT has long been regarded as simply a structural unit providing mechanical support to vasculature, it is now gaining reputation as an integral endocrine/paracrine component, in addition to the well-established modulator endothelium, in regulating vascular tone. Since the discovery of anti-contractile effect of PVAT in 1991, the use of multiple rodent models of reduced amounts of PVAT has revealed its regulatory role in vascular remodeling and cardiovascular implications, including atherosclerosis. PVAT does not only release PVAT-derived relaxing factors (PVRFs) to activate multiple subsets of endothelial and vascular smooth muscle potassium channels and anti-inflammatory signals in the vasculature, but it does also provide an interface for neuron-adipocyte interactions in the vascular wall to regulate arterial vascular tone. In this review, we outline our current understanding towards PVAT and attempt to provide hints about future studies that can sharpen the therapeutic potential of PVAT against cardiovascular diseases and their complications.


id: cord-010307-sxh5mq1q
author: MILNE, D. J.
date: 2005-11-23
txt: ./txt/cord-010307-sxh5mq1q.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7175956/
doi: 10.1111/j.1442-9993.2005.01535.x
summary:
  Abstract Patterns in the composition of assemblages of microbat species sampled during the late dry season (the ''build‐up'') in north Australian savannas were assessed against a range of environmental factors as well as four a priori defined habitat types (riparian, escarpments, coastal and woodlands). However, we expect this will have a negligible effect on our results as shot sampling at all other sites, used in conjunction with Anabat detectors, enabled us to collect an extensive reference call library for ''high-flying'' bat species for the entire study area (Milne 2002) . Group 5 also had relatively few sites and low species richness, but was associated with the minima or maxima of several environmental variables including long distances to escarpments, flat terrain at low elevations with no rock, low local roost potential, high annual temperatures and low fire frequency.

title:
  Structure and environmental relationships of insectivorous bat assemblages in tropical Australian savannas

abstract:
  Abstract Patterns in the composition of assemblages of microbat species sampled during the late dry season (the ‘build‐up’) in north Australian savannas were assessed against a range of environmental factors as well as four a priori defined habitat types (riparian, escarpments, coastal and woodlands). Distinct species assemblages were most strongly associated with topographic and climatic variables. There were also limited associations with vegetation structure, fire and local roost potential but no associations with insects or water availability. Total species diversity at sample sites was associated with distance to rivers and rainfall. In general, species assemblages were not clearly defined and the number of significant environmental associations was relatively few. We compare these associations with those reported for bat assemblages elsewhere in Australia.


id: cord-017407-nc9cyu2u
title: Introduction: The World of Bats
author: Mehlhorn, Heinz
date: 2013-09-03
txt: ./txt/cord-017407-nc9cyu2u.txt
cache: ./cache/cord-017407-nc9cyu2u.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121961/
doi: 10.1007/978-3-642-39333-4_1
summary:
  Bats are unique flying mammalians that occur worldwide feeding either on insects, fruits or even on blood depending on the species. Bats-their English name points to their fluttering up and down wing movementsare a peculiar group of the so-called Mammalia (¼ animals with breast nipples) in the Zoological System, where they are described as Chiroptera (Greek: cheir ¼ hand, pteron ¼ wing) (Neuweiler 1993; Niethammer and Krapp 2004, Claus et al. Bats are active at night seeking their food, which consistsdepending on the species-of insects, fruits or even of blood. Thus, their hidden way of life caused fear, especially in those cases, when many bats fly simultaneously around houses or around heads of persons, since they live together in groups of often more than 100-150 animals hiding themselves during daytime in the treetops (e.g. plant eating flying foxes e.g. in Australia) or in tunnels of railways, galleries of closed mines, in old, rottening empty buildings on practically all continents except for Antarctica.

abstract:
  Bats are unique flying mammalians that occur worldwide feeding either on insects, fruits or even on blood depending on the species. Since they are active during the night, many myths have been launched during the last 500 years. All these facets are shortly considered here and prepare for a hopefully intense look into their hidden life.


id: cord-017785-zwnkrs23
title: Mammalia: Chiroptera: Immunology of Bats
author: Baker, Michelle L.
date: 2018-03-10
txt: ./txt/cord-017785-zwnkrs23.txt
cache: ./cache/cord-017785-zwnkrs23.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122446/
doi: 10.1007/978-3-319-76768-0_23
summary:
  The role of bats as natural reservoirs of a variety of high-profile viruses that are highly pathogenic in other susceptible species yet cause no clinical disease in bats has led to a resurgence of interest in their immune systems. RNAseq studies on tissues and cells from a variety of different species of bats have provided evidence that bats have nearly all of the major components of the immune system that are present in other mammals, including receptors and molecules associated with innate and adaptive immunity and microRNAs (Papenfuss et al. Responses to antigens such as ϕX174 bacteriophage and sheep red blood cells have demonstrated that the generation of neutralizing antibodies is delayed in the big brown bat, the pteropid bat, and the Indian flying fox (Pteropus giganteus) (Hatten et al.

abstract:
  Bats are a large and diverse group comprising approximately 20% of all living mammalian species. They are the only mammals capable of powered flight and have many unique characteristics, including long lifespans, echolocation, and hibernation, and play key roles in insect control, pollination, and seed dispersal. The role of bats as natural reservoirs of a variety of high-profile viruses that are highly pathogenic in other susceptible species yet cause no clinical disease in bats has led to a resurgence of interest in their immune systems. Equally compelling is the urgency to understand the immune mechanisms responsible for the susceptibility of bats to the fungus responsible for white syndrome, which threatens to wipe out a number of species of North American bats. In this chapter we review the current knowledge in the field of bat immunology, focusing on recent highlights and the need for further investigations in this area.


id: cord-018821-e9oxvgar
title: Sociality, Parasites, and Pathogens in Bats
author: Webber, Quinn M. R.
date: 2016-04-27
txt: ./txt/cord-018821-e9oxvgar.txt
cache: ./cache/cord-018821-e9oxvgar.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123799/
doi: 10.1007/978-3-319-38953-0_5
summary:
  We identified social network analysis, epidemiological modeling, and interspecific comparative analyses as the most commonly used methods to quantify relationships between social behavior and parasite-risk in bats while WNS, Hendra virus, and arthropod ectoparasites were the most commonly studied host-parasite systems. Although the mechanism inducing increased energy expenditure and arousals by infected bats is still not fully understood (for review see Willis 2015) , variation in social behavior could mediate fungal transmission and growth, especially since affected species tend to hibernate in large colonies or aggregations in caves or mines. We suggest studies employing social network analysis of wild bats, combined with estimates of micro-and macroparasite prevalence, and intensity to disentangle relationships between host social behavior, including fission-fusion dynamics, and the ecology of parasite transmission (for review see Godfrey 2013). Ectoparasite studies have identified links between parasite risk, colony size, and fission-fusion dynamics which have broad implications for understanding how sociality affects host-parasite interactions in bats.

abstract:
  Little is known about the ecology of many of the parasites and pathogens affecting bats, but host social behavior almost certainly plays an important role in bat-parasite dynamics. Understanding parasite dynamics for bats is important from a human public health perspective because of their role as natural reservoirs for recent high-profile emerging zoonotic pathogens (e.g. Ebola, Hendra) and from a bat conservation perspective because of the recent emergence of white-nose syndrome (WNS) in North America highlighting the potential population impacts of parasites and pathogens. Although some bat species are among the most gregarious of mammals, species vary widely in terms of their social behavior and this variation could influence pathogen transmission and impacts. Here, we review the literature on links between bat social behavior and parasite dynamics. Using standardized search terms in Web of Science, we identified articles that explicitly tested or discussed links between some aspect of bat sociality and parasite transmission or host population impacts. We identified social network analysis, epidemiological modeling, and interspecific comparative analyses as the most commonly used methods to quantify relationships between social behavior and parasite-risk in bats while WNS, Hendra virus, and arthropod ectoparasites were the most commonly studied host-parasite systems. We summarize known host-parasite relationships in these three systems and propose testable hypotheses that could improve our understanding of links between host sociality and parasite-dynamics in bats.


id: cord-021152-6znmkvy9
title: Reproduction of East-African bats may guide risk mitigation for coronavirus spillover
author: Montecino-Latorre, Diego
date: 2020-02-07
txt: ./txt/cord-021152-6znmkvy9.txt
cache: ./cache/cord-021152-6znmkvy9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149079/
doi: 10.1186/s42522-019-0008-8
summary:
  METHODS: To assess the generalizability of coronavirus shedding seasonality, we sampled hundreds of bats belonging to several species with different life history traits across East Africa at different times of the year. Assuming that higher spillover risk is a function of higher viral shedding [67] and that all coronaviruses with zoonotic potential behave ecologically similarly to coronaviruses detected in this study, managers could target the prevention of human-bat direct (consumption) or indirect (bat droppings) contact specifically during the high-risk season: around and just after weaning, the timing of observable juveniles or individuals smaller than adults. Our proposed risk-driven strategy i) is evidence-based, as it builds upon coronavirus shedding patterns observed across several chiropteran species present around the world; ii) does not require the advanced laboratory capacity often lacking in resource-restricted settings where intense bat-human interfaces usually occur; iii) is a good alternative to the ideal but expensive and resourceintensive longitudinal surveys; and iv) it may prevent the exposure to viruses belonging to other taxa whose observed bat shedding dynamics resemble our findings for coronaviruses (e.g. paramyxoviruses [97] ),

abstract:
  BACKGROUND: Bats provide important ecosystem services; however, current evidence supports that they host several zoonotic viruses, including species of the Coronaviridae family. If bats in close interaction with humans host and shed coronaviruses with zoonotic potential, such as the Severe Acute Respiratory Syndrome virus, spillover may occur. Therefore, strategies aiming to mitigate potential spillover and disease emergence, while supporting the conservation of bats and their important ecological roles are needed. Past research suggests that coronavirus shedding in bats varies seasonally following their reproductive cycle; however, shedding dynamics have been assessed in only a few species, which does not allow for generalization of findings across bat taxa and geographic regions. METHODS: To assess the generalizability of coronavirus shedding seasonality, we sampled hundreds of bats belonging to several species with different life history traits across East Africa at different times of the year. We assessed, via Bayesian modeling, the hypothesis that chiropterans, across species and spatial domains, experience seasonal trends in coronavirus shedding as a function of the reproductive cycle. RESULTS: We found that, beyond spatial, taxonomic, and life history differences, coronavirus shedding is more expected when pups are becoming independent from the dam and that juvenile bats are prone to shed these viruses. CONCLUSIONS: These findings could guide policy aimed at the prevention of spillover in limited-resource settings, where longitudinal surveillance is not feasible, by identifying high-risk periods for coronavirus shedding. In these periods, contact with bats should be avoided (for example, by impeding or forbidding people access to caves). Our proposed strategy provides an alternative to culling – an ethically questionable practice that may result in higher pathogen levels – and supports the conservation of bats and the delivery of their key ecosystem services.


id: cord-021805-2j07zw6q
title: Emerging Diseases in Bats
author: Epstein, Jonathan H.
date: 2018-09-28
txt: ./txt/cord-021805-2j07zw6q.txt
cache: ./cache/cord-021805-2j07zw6q.txt
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mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152049/
doi: 10.1016/b978-0-323-55228-8.00040-0
abstract: nan
summary:
  6, 7 Bats have been associated with several zoonotic viruses that have recently been discovered and linked to significant human and animal disease, including severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), Ebola and Marburg viruses, and Nipah virus (NiV) 8 (see also Chapters 19, 34, and 42 ). Viral discovery has, however, significantly expanded our understanding of the phylogenetic breadth of important viral families such as filoviruses (e.g., Ebola virus), paramyxoviruses (e.g., NiV), and coronaviruses (e.g., SARS coronavirus [CoV]), which is necessary for both better understanding what makes viruses pathogenic and also for recognizing wildlife reservoirs of viral pathogens, once they do emerge, more rapidly. Data are mounting to support bats as important reservoirs compared with other mammals, and large-scale surveillance efforts like PREDICT and the recently launched Global Virome Project, a 10-year effort to identify the majority of viruses in key wildlife species in emerging disease hot spots, 73 will shed more light on the total diversity of viruses in bat species and the types of human-animal interfaces that exist in different geographic and cultural contexts.


id: cord-102977-yci9kq6x
title: GHSR-1a is not Required for Ghrelin’s Anti-inflammatory and Fat-sparing Effects in Cancer Cachexia
author: Liu, Haiming
date: 2019-12-06
txt: ./txt/cord-102977-yci9kq6x.txt
cache: ./cache/cord-102977-yci9kq6x.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/866376
doi: 10.1101/866376
summary:
  This study characterizes the pathways involved in AT atrophy in the Lewis Lung Carcinoma (LLC)-induced cachexia model and those mediating the effects of ghrelin in Ghsr+/+ and Ghsr−/− mice. GHSR-1a is not expressed in adipocytes (Sun, Garcia et 243 al., 2007) but is present in macrophages (Ma, Lin et al., 2013) and our findings are consistent with a 244 previous report showing that old, non-tumor-bearing Ghsr -/mice have reduced macrophage 245 infiltration, a shift on macrophage differentiation towards a more anti-inflammatory phenotype, and 246 decreased inflammation in adipose tissue (Lin, Lee et al., 2016) . In this study, we did 278 not see a significant effect of ghrelin on preventing LLC-induced fat browning, BAT thermogenesis, 279 increased REE or decreased physical activity in the setting of CACS despite the fact that ghrelin 280 prevented fat and weight loss and anorexia.

abstract:
  Adipose tissue (AT) atrophy is a hallmark of cancer cachexia contributing to increased morbidity/mortality. Ghrelin has been proposed as a treatment for cancer cachexia partly by preventing AT atrophy. However, the mechanisms mediating ghrelin’s effects are incompletely understood, including the extent to which its only known receptor, GHSR-1a, is required for these effects. This study characterizes the pathways involved in AT atrophy in the Lewis Lung Carcinoma (LLC)-induced cachexia model and those mediating the effects of ghrelin in Ghsr+/+ and Ghsr−/− mice. We show that LLC causes AT atrophy by inducing anorexia, and increasing AT inflammation, thermogenesis and energy expenditure. These changes were greater in Ghsr−/−. Ghrelin administration prevented LLC-induced anorexia only in Ghsr+/+, but prevented WAT inflammation and atrophy in both genotypes, although its effects were greater in Ghsr+/+. LLC-induced increases in BAT inflammation, WAT and BAT thermogenesis, and energy expenditure were not affected by ghrelin. In conclusion, ghrelin ameliorates WAT inflammation, fat atrophy and anorexia in LLC-induced cachexia. GHSR-1a is required for ghrelin’s orexigenic effect but not for its anti-inflammatory or fat-sparing effects.


id: cord-103460-5thh6syt
title: Climate change will drive novel cross-species viral transmission
author: Carlson, Colin J.
date: 2020-07-14
txt: ./txt/cord-103460-5thh6syt.txt
cache: ./cache/cord-103460-5thh6syt.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.01.24.918755
doi: 10.1101/2020.01.24.918755
summary:
  In addition, changing climate and land use are already driving geographic range shifts in wildlife, producing novel species assemblages and opportunities for viral sharing between previously isolated species4,5. Here, we map potential hotspots of viral sharing, using a phylogeographic model of the mammal-virus network, and projections of geographic range shifts for 3,870 mammal species under climate change and land use scenarios for the year 2070. Range-shifting mammal species are predicted to aggregate at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, driving the cross-species transmission of novel viruses at least 4,000 times. Even with dispersal limits, these first encounters are predicted to produce al-207 most one hundred new viral sharing events (RCP 2.6: 96 ± 2.3; RCP 8.5: 86 ± 3.9) that might 208 include ZEBOV, and which cover a much broader part of Africa than the current zoonotic niche 209 of Ebola 68 .

abstract:
  At least 10,000 species of mammal virus are estimated to have the potential to spread in human populations, but the vast majority are currently circulating in wildlife, largely undescribed and undetected by disease outbreak surveillance1,2,3. In addition, changing climate and land use are already driving geographic range shifts in wildlife, producing novel species assemblages and opportunities for viral sharing between previously isolated species4,5. In some cases, this will inevitably facilitate spillover into humans6,7—a possible mechanistic link between global environmental change and emerging zoonotic disease8. Here, we map potential hotspots of viral sharing, using a phylogeographic model of the mammal-virus network, and projections of geographic range shifts for 3,870 mammal species under climate change and land use scenarios for the year 2070. Range-shifting mammal species are predicted to aggregate at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, driving the cross-species transmission of novel viruses at least 4,000 times. Counter to expectations, holding warming under 2°C within the century does not reduce new viral sharing, due to greater range expansions—highlighting the need to invest in surveillance even in a low-warming future. Most projected viral sharing is driven by diverse hyperreservoirs (rodents and bats) and large-bodied predators (carnivores). Because of their unique dispersal capacity, bats account for the majority of novel viral sharing, and are likely to share viruses along evolutionary pathways that could facilitate future emergence in humans. Our findings highlight the urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking range shifts, especially in tropical countries that harbor the most emerging zoonoses.


id: cord-254543-gxwtqqdu
title: Bat consumption in Thailand
author: Suwannarong, Kanokwan
date: 2016-01-22
txt: ./txt/cord-254543-gxwtqqdu.txt
cache: ./cache/cord-254543-gxwtqqdu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26806167/
doi: 10.3402/iee.v6.29941
summary:
  Communities in which bat guano is mined from caves have extensive exposure to bat excreta, often harvest bats for consumption, and are at risk for bat-borne diseases. METHODS: This rapid ethnographic study was conducted in four provinces of Thailand (Ratchaburi, Sakaeo, Nakorn Sawan, and Phitsanulok), where bat guano was mined and sold during the period April–August 2014. There is an opportunity to reduce the risk of bat-borne diseases in guano-mining communities by strengthening bat conservation efforts and raising awareness of the health risks of bat consumption. Because of the potential for human contact with infected bats, the PREVENT Project, a part of the US Agency for International Development''s (USAID) Emerging Pandemic Threats (EPT) Program, decided to conduct this exploratory, rapid ethnographic study. The sites, located in four provinces (Ratchaburi, Sakaeo, Nakorn Sawan, and Phitsanulok), were selected to represent several different ways in which bat guano mining is organized and regulated.

abstract:
  BACKGROUND: Human consumption of bats poses an increasing public health threat globally. Communities in which bat guano is mined from caves have extensive exposure to bat excreta, often harvest bats for consumption, and are at risk for bat-borne diseases. METHODS: This rapid ethnographic study was conducted in four provinces of Thailand (Ratchaburi, Sakaeo, Nakorn Sawan, and Phitsanulok), where bat guano was mined and sold during the period April–August 2014. The aim of this study was to understand behaviors and risk perceptions associated with bat conservation, exposure to bats and their excreta, and bat consumption. Sixty-seven respondents playing various roles in bat guano mining, packaging, sale, and use as fertilizer participated in the study. Data were collected through interviews and/or focus group discussions. RESULTS: In spite of a bat conservation program dating back to the 1980s, the benefits of conserving bats and the risks associated with bat consumption were not clear and infrequently articulated by study respondents. DISCUSSION: Since bat consumption continues, albeit covertly, the risk of bat-borne diseases remains high. There is an opportunity to reduce the risk of bat-borne diseases in guano-mining communities by strengthening bat conservation efforts and raising awareness of the health risks of bat consumption. Further research is suggested to test behavior change strategies for reducing bat consumption.


id: cord-254713-ghcwfcx2
title: Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar
author: Razanajatovo, Norosoa H
date: 2015-03-12
txt: ./txt/cord-254713-ghcwfcx2.txt
cache: ./cache/cord-254713-ghcwfcx2.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12985-015-0271-y
doi: 10.1186/s12985-015-0271-y
summary:
  RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Studies which aimed to identify potential reservoirs of emerging human CoVs have revealed that the Betacoronavirus SARS-CoV was closely related to CoVs detected in bats, specifically members of the genus (Rhinolophus), which brought the hypothesis of a spillover of this virus to several animal species (including civet cats and raccoons) sold in Chinese markets as bushmeat for human consumption [9] [10] [11] . A total of 351 bats belonging to 3 endemic bat species of the family Pteropodidae were captured and sampled: Rousettus madagascariensis (n = 179), Pteropus rufus (n = 76) and Eidolon dupreanum (n = 96) ( Table 1) . In the context of this study, we detected 14 coronaviruses forming nine genetically distinct strains in two endemic Malagasy frugivorous bat species.

abstract:
  BACKGROUND: Bats are amongst the natural reservoirs of many coronaviruses (CoVs) of which some can lead to severe infection in human. African bats are known to harbor a range of pathogens (e.g., Ebola and Marburg viruses) that can infect humans and cause disease outbreaks. A recent study in South Africa isolated a genetic variant closely related to MERS-CoV from an insectivorous bat. Though Madagascar is home to 44 bat species (41 insectivorous and 3 frugivorous) of which 34 are endemic, no data exists concerning the circulation of CoVs in the island’s chiropteran fauna. Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat. The purpose of our study is to detect and identify CoVs from frugivorous bats in Madagascar to evaluate the risk of human infection from infected bats. METHODS: Frugivorous bats belonging to three species were captured in four different regions of Madagascar. We analyzed fecal and throat swabs to detect the presence of virus through amplification of the RNA-dependent RNA polymerase (RdRp) gene, which is highly conserved in all known coronaviruses. Phylogenetic analyses were performed from positive specimens. RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Phylogenetic analysis revealed that the Malagasy strains belong to the genus Betacoronavirus but form three distinct clusters, which seem to represent previously undescribed genetic lineages. CONCLUSIONS: Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats. Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed.


id: cord-255137-utg8k7qs
author: Yinda, Claude Kwe
date: 2019-01-23
txt: ./txt/cord-255137-utg8k7qs.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30674646/
doi: 10.1128/msphere.00585-18
summary:
  Previously, we identified a plethora of known and novel eukaryotic viruses in Cameroonian fruit bats using a viral metagenomics approach, including viruses known to cause gastroenteritis in humans (sapovirus, sapelovirus, and rotaviruses A and H) and Astroviridae (Mamastrovirus), Calciviridae (Sapovirus), Picornaviridae (Parechovirus), and Reoviridae (Rotavirus), viral families known to cause gastroenteritis in humans, were identified in both bat and human pools from the same region. In this study, we focused on viruses from which near-complete genomes were obtained, particularly those that are known to cause viral gastroenteritis (belonging to the Astroviridae, Caliciviridae [norovirus and sapovirus] , Picornaviridae [enterovirus, parechovirus, cosavirus] , Parvoviridae, Reoviridae, and Adenoviridae [human mastadenovirus]). Recently, we thoroughly investigated the gut virome of fruit bats from Cameroon (20) (21) (22) (23) 63) and showed the presence of many novel and divergent eukaryotic viral families, including viruses known to cause gastroenteritis in humans.

title:
  Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses

abstract:
  Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases of diarrhea are likely caused by yet-unidentified viral agents, some of which could be the result of (recent) interspecies transmission from animal reservoirs, like bats. Using viral metagenomics, we screened fecal samples of 221 humans (almost all with gastroenteritis symptoms) between 0 and 89 years of age with different degrees of bat contact. We identified viruses belonging to families that are known to cause gastroenteritis such as Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, and Reoviridae. Interestingly, a mammalian orthoreovirus, picobirnaviruses, a smacovirus, and a pecovirus were also found. Although there was no evidence of interspecies transmission of the most common human gastroenteritis-related viruses (Astroviridae, Caliciviridae, and Reoviridae), the phylogenies of the identified orthoreovirus, picobirnavirus, and smacovirus indicate a genetic relatedness of these viruses identified in stools of humans and those of bats and/or other animals. These findings points out the possibility of interspecies transmission or simply a shared host of these viruses (bacterial, fungal, parasitic, …) present in both animals (bats) and humans. Further screening of bat viruses in humans or vice versa will elucidate the epidemiological potential threats of animal viruses to human health. Furthermore, this study showed a huge diversity of highly divergent novel phages, thereby expanding the existing phageome considerably. IMPORTANCE Despite the availability of diagnostic tools for different enteric viral pathogens, a large fraction of human cases of gastroenteritis remains unexplained. This could be due to pathogens not tested for or novel divergent viruses of potential animal origin. Fecal virome analyses of Cameroonians showed a very diverse group of viruses, some of which are genetically related to those identified in animals. This is the first attempt to describe the gut virome of humans from Cameroon. Therefore, the data represent a baseline for future studies on enteric viral pathogens in this area and contribute to our knowledge of the world’s virome. The studies also highlight the fact that more viruses may be associated with diarrhea than the typical known ones. Hence, it provides meaningful epidemiological information on diarrhea-related viruses in this area.


id: cord-256370-cz88t29n
title: Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa
author: Jansen van Vuren, Petrus
date: 2016-02-29
txt: ./txt/cord-256370-cz88t29n.txt
cache: ./cache/cord-256370-cz88t29n.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v8030065
doi: 10.3390/v8030065
summary:
  This is the first report on isolation of an orthoreovirus from an arthropod host associated with bats, and phylogenetic and sequence data suggests that MAHLV constitutes a new species within the Orthoreovirus genus. Maximum Likelihood trees were prepared using amino acid sequences of all open reading frames from all segments, showing the placement of Mahlapitsi virus (MAHLV) in the Orthoreovirus genus relative to other viruses in this genus for which sequence is available on Genbank. A Maximum Likelihood tree, constructed with nucleic acid sequence data for the RNA-dependent RNA polymerase (RdRp) encoding segments of representative viruses from the different genera within Reoviridae (Figure 7) shows the placement of both isolates amongst other orthoreoviruses in the family. Maximum Likelihood trees were prepared using the deduced amino acid sequences from the open reading frames (ORF''s) of all the virus'' segments and those of other viruses in the Orthoreovirus genus (Figures 8-10) .

abstract:
  We report on the isolation of a novel fusogenic orthoreovirus from bat flies (Eucampsipoda africana) associated with Egyptian fruit bats (Rousettus aegyptiacus) collected in South Africa. Complete sequences of the ten dsRNA genome segments of the virus, tentatively named Mahlapitsi virus (MAHLV), were determined. Phylogenetic analysis places this virus into a distinct clade with Baboon orthoreovirus, Bush viper reovirus and the bat-associated Broome virus. All genome segments of MAHLV contain a 5' terminal sequence (5'-GGUCA) that is unique to all currently described viruses of the genus. The smallest genome segment is bicistronic encoding for a 14 kDa protein similar to p14 membrane fusion protein of Bush viper reovirus and an 18 kDa protein similar to p16 non-structural protein of Baboon orthoreovirus. This is the first report on isolation of an orthoreovirus from an arthropod host associated with bats, and phylogenetic and sequence data suggests that MAHLV constitutes a new species within the Orthoreovirus genus.


id: cord-256452-77xij0fc
author: Allen, Louise C.
date: 2008-11-11
txt: ./txt/cord-256452-77xij0fc.txt
cache: ./cache/cord-256452-77xij0fc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00360-008-0315-3
doi: 10.1007/s00360-008-0315-3
summary:
  title: Roosting ecology and variation in adaptive and innate immune system function in the Brazilian free-tailed bat (Tadarida brasiliensis) We examined aspects of both innate and adaptive immune response in adult female Brazilian free-tailed bats (Tadarida brasiliensis) at four maternity roosts (two natural caves and two human-made bridges) in south-central Texas. The Brazilian free-tailed bat (Tadarida brasiliensis), for example, roosts in some of the largest aggregations of mammals on earth, with several thousand to several million individual bats estimated to form maternity colonies in caves and under highway bridges (Davis et al. Determining the ecological factors that predict variation in the ability of individual Brazilian free-tailed bats to exhibit functional immunological responses is important to understand disease dynamics and population health in this and other species of colonial animals.

title:
  Roosting ecology and variation in adaptive and innate immune system function in the Brazilian free-tailed bat (Tadarida brasiliensis)

abstract:
  Bats have recently been implicated as reservoirs of important emerging diseases. However, few studies have examined immune responses in bats, and even fewer have evaluated these responses in an ecological context. We examined aspects of both innate and adaptive immune response in adult female Brazilian free-tailed bats (Tadarida brasiliensis) at four maternity roosts (two natural caves and two human-made bridges) in south-central Texas. Immune measurements included in vitro bactericidal ability of whole blood and in vivo T cell mediated response to mitogenic challenge. Bactericidal activity in T. brasiliensis varied with roosting ecology, but appears to be sensitive to colony-level effects. Blood from females living at one cave had significantly lower bactericidal ability than blood from females at three other sites. T cell mediated response in this species was associated with variation in roost ecology, with females from two caves having greater responses than females from two bridges. T cell mediated response and bactericidal activity were negatively correlated with one another within individuals that were tested for both. Variation in immunological response of T. brasiliensis is important for understanding the influence of the environment on the frequency and distribution of immunologically competent individuals and for understanding disease-host dynamics in this and other colonial species.


id: cord-257321-l1swyr6g
title: DRodVir: A resource for exploring the virome diversity in rodents
author: Chen, Lihong
date: 2017-05-20
txt: ./txt/cord-257321-l1swyr6g.txt
cache: ./cache/cord-257321-l1swyr6g.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28533016/
doi: 10.1016/j.jgg.2017.04.004
summary:
  The database currently covers 7690 sequences from 5491 rodent-associated mammal viruses of 26 viral families detected from 194 rodent species in 93 countries worldwide. As a data application example, we further compared the current status of rodent-associated viruses with bat-associated viruses to highlight the necessity for including additional host species and geographic regions in future investigations, which will help us achieve a better understanding of the virome diversities in the two major reservoirs of emerging zoonotic infectious diseases. To facilitate online data analysis, two visualization tools are integrated into the result table: i) a statistical pie chart is available with a single click on the column title of virus family, rodent species/family, sample type and sampling country (Fig. 2B) ; ii) a global map with indicative markers is provided for the column of sampling country to better illustrate the geographic distribution of the rodent-associated viruses (http://www.mgc.ac.

abstract:
  Emerging zoonotic diseases have received tremendous interests in recent years, as they pose a significant threat to human health, animal welfare, and economic stability. A high proportion of zoonoses originate from wildlife reservoirs. Rodents are the most numerous, widespread, and diverse group of mammals on the earth and are reservoirs for many zoonotic viruses responsible for significant morbidity and mortality. A better understanding of virome diversity in rodents would be of importance for researchers and professionals in the field. Therefore, we developed the DRodVir database (http://www.mgc.ac.cn/DRodVir/), a comprehensive, up-to-date, and well-curated repository of rodent-associated animal viruses. The database currently covers 7690 sequences from 5491 rodent-associated mammal viruses of 26 viral families detected from 194 rodent species in 93 countries worldwide. In addition to virus sequences, the database provides detailed information on related samples and host rodents, as well as a set of online analytical tools for text query, BLAST search and phylogenetic reconstruction. The DRodVir database will help virologists better understand the virome diversity of rodents. Moreover, it will be a valuable tool for epidemiologists and zoologists for easy monitoring and tracking of the current and future zoonotic diseases. As a data application example, we further compared the current status of rodent-associated viruses with bat-associated viruses to highlight the necessity for including additional host species and geographic regions in future investigations, which will help us achieve a better understanding of the virome diversities in the two major reservoirs of emerging zoonotic infectious diseases.


id: cord-258160-v08cs51n
title: Review of Bats and SARS
author: Wang, Lin-Fa
date: 2006-12-17
txt: ./txt/cord-258160-v08cs51n.txt
cache: ./cache/cord-258160-v08cs51n.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/17326933/
doi: 10.3201/eid1212.060401
summary:
  Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Although in 1 live animal market, 3 species were found to be infected by viruses related to SARS-CoV (9), all subsequent studies have focused mainly on palm civets, possibly because the rate of detection was higher in civets or because the number of civets traded in southern People''s Republic of China exceeds that of other wildlife groups.

abstract:
  Bats have been identified as a natural reservoir for an increasing number of emerging zoonotic viruses, including henipaviruses and variants of rabies viruses. Recently, we and another group independently identified several horseshoe bat species (genus Rhinolophus) as the reservoir host for a large number of viruses that have a close genetic relationship with the coronavirus associated with severe acute respiratory syndrome (SARS). Our current research focused on the identification of the reservoir species for the progenitor virus of the SARS coronaviruses responsible for outbreaks during 2002–2003 and 2003–2004. In addition to SARS-like coronaviruses, many other novel bat coronaviruses, which belong to groups 1 and 2 of the 3 existing coronavirus groups, have been detected by PCR. The discovery of bat SARS-like coronaviruses and the great genetic diversity of coronaviruses in bats have shed new light on the origin and transmission of SARS coronaviruses.


id: cord-261547-8tfbhmzo
title: Genetic diversity of bats coronaviruses in the Atlantic Forest hotspot biome, Brazil
author: Góes, Luiz Gustavo Bentim
date: 2016-07-26
txt: ./txt/cord-261547-8tfbhmzo.txt
cache: ./cache/cord-261547-8tfbhmzo.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134816303240
doi: 10.1016/j.meegid.2016.07.034
summary:
  In this report, we identified and characterized previously unknown and diverse genetic clusters of bat coronaviruses in the Atlantic Forest Biome, Brazil. Recently, a number of novel bats CoVs have been identified, primarily from African, Asian and European bats (Calisher et al., 2006; Chu et al., 2006; Drexler et al., 2014) , as well as from South American countries including Costa Rica, Panama, Ecuador, Mexico and Brazil (Corman et al., 2013; Goes et al., 2013) . Coronaviruses were detected in 15 bat intestines samples from eight bat species with distinct diet habit, demonstrating a marked potential of CoVs distribution among bat species in AFB that harbours 9% of world''s bat diversity. α-CoV sequences obtained from bats of same genus presented high nucleotide sequence similarity (e.g. Artibeus, Glossophaga, Carollia, Molossus, Myotis and Sturnira) (Fig. 1D and Supplementary table), even with sequences detected in other studies from bats of geographically distant regions. It is indispensable in future to investigate the evolutionary events in genetically diverse bats CoVs using complete genome sequences, and their possible transmission potentials to human being.

abstract:
  Bats are notorious reservoirs of genetically-diverse and high-profile pathogens, and are playing crucial roles in the emergence and re-emergence of viruses, both in human and in animals. In this report, we identified and characterized previously unknown and diverse genetic clusters of bat coronaviruses in the Atlantic Forest Biome, Brazil. These results highlight the virus richness of bats and their possible roles in the public health.


id: cord-262434-q4tk96tq
title: Poxviruses in Bats … so What?
author: Baker, Kate S.
date: 2014-04-03
txt: ./txt/cord-262434-q4tk96tq.txt
cache: ./cache/cord-262434-q4tk96tq.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v6041564
doi: 10.3390/v6041564
summary:
  Finally, we speculate on the possible consequences and potential research avenues opened following this marrying of a pathogen of great historical and contemporary importance with an ancient host that has an apparently peculiar relationship with viruses; a fascinating and likely fruitful meeting whose study will be facilitated by recent technological advances and a heightened interest in bat virology. Similarly, testing the in vitro host range of isolated viruses such as Eptesipox virus would help inform whether human and further animal cell lines are permissive for infection (i.e., that they contain the necessary host factors to support infection and do not contain antiviral components that restrict infection). Further field (in situ), in vitro and in silico studies could elucidate the possible coevolution, cross species infections and mechanisms of host range restriction of bat poxviruses, the implications of which are relevant for bat ecologists, virologists and emerging infectious disease specialists (including those with a specific interest in bats) alike.

abstract:
  Poxviruses are important pathogens of man and numerous domestic and wild animal species. Cross species (including zoonotic) poxvirus infections can have drastic consequences for the recipient host. Bats are a diverse order of mammals known to carry lethal viral zoonoses such as Rabies, Hendra, Nipah, and SARS. Consequent targeted research is revealing bats to be infected with a rich diversity of novel viruses. Poxviruses were recently identified in bats and the settings in which they were found were dramatically different. Here, we review the natural history of poxviruses in bats and highlight the relationship of the viruses to each other and their context in the Poxviridae family. In addition to considering the zoonotic potential of these viruses, we reflect on the broader implications of these findings. Specifically, the potential to explore and exploit this newfound relationship to study coevolution and cross species transmission together with fundamental aspects of poxvirus host tropism as well as bat virology and immunology.


id: cord-262815-fg76s168
title: Coronaviruses in bats from Mexico
author: Anthony, S. J.
date: 2013-05-01
txt: ./txt/cord-262815-fg76s168.txt
cache: ./cache/cord-262815-fg76s168.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1099/vir.0.049759-0
doi: 10.1099/vir.0.049759-0
summary:
  Analyses of these viruses in the context of their hosts and ecological habitat indicated that host species is a strong selective driver in CoV evolution, even in allopatric populations separated by significant geographical distance; and that a single species/genus of bat can contain multiple CoVs. A β-CoV with 96.5 % amino acid identity to the β-CoV associated with human disease in the Middle East was found in a Nyctinomops laticaudatus bat, suggesting that efforts to identify the viral reservoir should include surveillance of the bat families Molossidae/Vespertilionidae, or the closely related Nycteridae/Emballonuridae. Several of the novel CoVs described in the last decade were identified in bats of various species and demonstrate a strong association between bats and CoVs (August et al., 2012; Carrington et al., 2008; Chu et al., 2009; Dominguez et al., 2007; Drexler et al., 2011 Drexler et al., , 2010 Falcó n et al., 2011; Ge et al., 2012b; Gloza-Rausch et al., 2008; Li et al., 2005; Misra et al., 2009; Osborne et al., 2011; Pfefferle et al., 2009; Quan et al., 2010; Reusken et al., 2010; Tong et al., 2009b; Woo et al., 2006; Yuan et al., 2010) .

abstract:
  Bats are reservoirs for a wide range of human pathogens including Nipah, Hendra, rabies, Ebola, Marburg and severe acute respiratory syndrome coronavirus (CoV). The recent implication of a novel beta (β)-CoV as the cause of fatal respiratory disease in the Middle East emphasizes the importance of surveillance for CoVs that have potential to move from bats into the human population. In a screen of 606 bats from 42 different species in Campeche, Chiapas and Mexico City we identified 13 distinct CoVs. Nine were alpha (α)-CoVs; four were β-CoVs. Twelve were novel. Analyses of these viruses in the context of their hosts and ecological habitat indicated that host species is a strong selective driver in CoV evolution, even in allopatric populations separated by significant geographical distance; and that a single species/genus of bat can contain multiple CoVs. A β-CoV with 96.5 % amino acid identity to the β-CoV associated with human disease in the Middle East was found in a Nyctinomops laticaudatus bat, suggesting that efforts to identify the viral reservoir should include surveillance of the bat families Molossidae/Vespertilionidae, or the closely related Nycteridae/Emballonuridae. While it is important to investigate unknown viral diversity in bats, it is also important to remember that the majority of viruses they carry will not pose any clinical risk, and bats should not be stigmatized ubiquitously as significant threats to public health.


id: cord-265357-3f0xph0y
author: Halczok, Tanja K.
date: 2017-01-05
txt: ./txt/cord-265357-3f0xph0y.txt
cache: ./cache/cord-265357-3f0xph0y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28056776/
doi: 10.1186/s12862-016-0856-0
summary:
  RESULTS: We used 19 nuclear and one mitochondrial microsatellite loci to analyze the genetic population structure of the Natterer''s bat (Myotis nattereri) within and among populations at different geographical scales in Germany. CONCLUSIONS: The genetic population structure of the bat host suggests that mating sites where several local breeding colonies meet act as stepping-stones for gene flow. We studied patterns of population genetic structure and dispersal of Myotis nattereri within and among three geographic regions of Germany using both nuclear and mitochondrial microsatellite markers. We hypothesized that if virus transmission between host populations were associated with events linked to gene flow in the bats, e.g. mating [28] , genetic co-variation should be detectable between host populations and astroviruses on a larger scale (e.g. between geographic regions), even though not necessarily within a certain region. Using the 19 autosomal microsatellite loci, Structure inferred the presence of three distinct genetic clusters ( Fig. 2 ; Additional file 1: Figure S1 ), splitting our data set into the three sampled regions NRW, MV and BY.

title:
  Evidence for genetic variation in Natterer’s bats (Myotis nattereri) across three regions in Germany but no evidence for co-variation with their associated astroviruses

abstract:
  BACKGROUND: As bats have recently been described to harbor many different viruses, several studies have investigated the genetic co-variation between viruses and different bat species. However, little is known about the genetic co-variation of viruses and different populations of the same bat species, although such information is needed for an understanding of virus transmission dynamics within a given host species. We hypothesized that if virus transmission between host populations depends on events linked to gene flow in the bats, genetic co-variation should exist between host populations and astroviruses. RESULTS: We used 19 nuclear and one mitochondrial microsatellite loci to analyze the genetic population structure of the Natterer’s bat (Myotis nattereri) within and among populations at different geographical scales in Germany. Further, we correlated the observed bat population structure to that of partial astrovirus sequences (323–394 nt fragments of the RNA-dependent RNA polymerase gene) obtained from the same bat populations. Our analyses revealed that the studied bat colonies can be grouped into three distinct genetic clusters, corresponding to the three geographic regions sampled. Furthermore, we observed an overall isolation-by-distance pattern, while no significant pattern was observed within a geographic region. Moreover, we found no correlation between the genetic distances among the bat populations and the astrovirus sequences they harbored. Even though high genetic similarity of some of the astrovirus haplotypes found in several different regions was detected, identical astrovirus haplotypes were not shared between different sampled regions. CONCLUSIONS: The genetic population structure of the bat host suggests that mating sites where several local breeding colonies meet act as stepping-stones for gene flow. Identical astrovirus haplotypes were not shared between different sampled regions suggesting that astroviruses are mostly transmitted among host colonies at the local scale. Nevertheless, high genetic similarity of some of the astrovirus haplotypes found in several different regions implies that occasional transmission across regions with subsequent mutations of the virus haplotypes does occur. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-016-0856-0) contains supplementary material, which is available to authorized users.


id: cord-268645-5op2m7pu
author: Wu, Zhiqiang
date: 2015-08-11
txt: ./txt/cord-268645-5op2m7pu.txt
cache: ./cache/cord-268645-5op2m7pu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26262818/
doi: 10.1038/ismej.2015.138
summary:
  However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. Based on the partial genomic sequences of the viruses obtained by the assembly, we designed specific nested primers for PCR or reverse trancriptase-PCR to screen for each virus in individual samples from each bat species (the primer sequences for each virus are available in Supplementary Table S2 ). The diverse BtCoVs were grouped into several novel evolutionary clades that significantly differed from those of all known αand β-CoVs, providing additional evidence to support investigations of the evolution of bat-originated CoVs. With regard to BtParaVs, a previous study has revealed that bats host major mammalian ParaVs in the genera Rubulavirus, Morbillivirus, Henipavirus and the subfamily Pneumovirinae (Drexler et al., 2012) .

title:
  Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases

abstract:
  Studies have demonstrated that ~60%–80% of emerging infectious diseases (EIDs) in humans originated from wild life. Bats are natural reservoirs of a large variety of viruses, including many important zoonotic viruses that cause severe diseases in humans and domestic animals. However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. The purpose of this study was to survey the ecological and biological diversities of viruses residing in these bat species, to investigate the presence of potential bat-borne zoonotic viruses and to evaluate the impacts of these viruses on public health. The data obtained in this study revealed an overview of the viral community present in these bat samples. Many novel bat viruses were reported for the first time and some bat viruses closely related to known human or animal pathogens were identified. This genetic evidence provides new clues in the search for the origin or evolution pattern of certain viruses, such as coronaviruses and noroviruses. These data offer meaningful ecological information for predicting and tracing wildlife-originated EIDs.


id: cord-270143-muxrxvyo
title: Paramyxo- and Coronaviruses in Rwandan Bats
author: Markotter, Wanda
date: 2019-07-02
txt: ./txt/cord-270143-muxrxvyo.txt
cache: ./cache/cord-270143-muxrxvyo.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/tropicalmed4030099
doi: 10.3390/tropicalmed4030099
summary:
  A high diversity of coronaand paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of coronaand paramyxoviral RNA using reverse transcription PCR assays. Although several surveillance studies have been implemented to detect potential zoonotic viruses in bats, including from countries in the Congo basin and East Africa, limited information is available for Rwanda. Confirmation of species identification of bats, in which viral RNA was detected, was performed by amplifying the cytochrome b (cyt b) or cytochrome oxidase one (COI) gene region and determining the DNA sequence. aegyptiacus-derived viral sequence (BatPV/Rou_aeg/UP438/RWA/2008) grouped within a Henipavirus-related clade and was near identical to a paramyxoviral sequence detected in the same host species previously reported from Kenya [36] .

abstract:
  A high diversity of corona- and paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of corona- and paramyxoviral RNA using reverse transcription PCR assays. Positive results were further characterized by DNA sequencing and phylogenetic analysis. In addition to morphological identification of bat species, we also did molecular confirmation of species identities, contributing to the known genetic database available for African bat species. We detected a novel Betacoronavirus in two Geoffroy’s horseshoe bats (Rhinolophus clivosus) bats. We also detected several different paramyxoviral species from various insectivorous bats. One of these viral species was found to be homologous to the genomes of viruses belonging to the Jeilongvirus genus. Additionally, a Henipavirus-related sequence was detected in an Egyptian rousette fruit bat (Rousettus aegyptiacus). These results expand on the known diversity of corona- and paramyxoviruses and their geographical distribution in Africa.


id: cord-270335-8vqi9c68
title: Rousettus aegyptiacus Bats Do Not Support Productive Nipah Virus Replication
author: Seifert, Stephanie N
date: 2019-11-04
txt: ./txt/cord-270335-8vqi9c68.txt
cache: ./cache/cord-270335-8vqi9c68.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/infdis/jiz429
doi: 10.1093/infdis/jiz429
summary:
  Nipah virus is capable of infecting a broad range of hosts including humans, pigs, ferrets, dogs, cats, hamsters, and at least 2 genera of bats. Studies of wild caught Pteropus spp suggest potential for viral recrudescence [16, 23] ; however, the hypothesis that NiV may persist in an individual bat and re-emerge under times of stress has yet to be confirmed experimentally. In contrast, the Egyptian fruit bat (EFB), Rousettus aegyptiacus, belongs to the same taxonomic family as Pteropus spp, Pteropodidae, and has been successfully used to model Marburg virus transmission [24, 25] and serological cross-reactivity after filovirus challenge [26] . Previous studies have demonstrated that EFB cells are permissive to Ebola virus, but experimentally challenged bats did not shed virus or support productive replication [38, 39] despite compatibility between the Ebola virus glycoprotein and the host receptor, NPC1 [40] .

abstract:
  Nipah virus (NiV) is a bat-borne zoonotic pathogen that can cause severe respiratory distress and encephalitis upon spillover into humans. Nipah virus is capable of infecting a broad range of hosts including humans, pigs, ferrets, dogs, cats, hamsters, and at least 2 genera of bats. Little is known about the biology of NiV in the bat reservoir. In this study, we evaluate the potential for the Egyptian fruit bat (EFB), Rousettus aegyptiacus, to serve as a model organism for studying NiV in bats. Our data suggest that NiV does not efficiently replicate in EFBs in vivo. Furthermore, we show a lack of seroconversion against NiV glycoprotein and a lack of viral replication in primary and immortalized EFB-derived cell lines. Our data show that despite using a conserved target for viral entry, NiV replication is limited in some bat species. We conclude that EFBs are not an appropriate organism to model NiV infection or transmission in bats.


id: cord-270803-jtv5jmkn
author: Wang, Lin-Fa
date: 2011-11-09
txt: ./txt/cord-270803-jtv5jmkn.txt
cache: ./cache/cord-270803-jtv5jmkn.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1879625711001325
doi: 10.1016/j.coviro.2011.10.013
summary:
  This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. Bats (order Chiroptera), one of the most abundant, diverse and geographically dispersed vertebrates on earth, have recently been shown to be reservoir hosts of a number of emerging viruses responsible for severe disease outbreaks in humans and livestock [1 ,2,3].

title:
  Mass extinctions, biodiversity and mitochondrial function: are bats ‘special’ as reservoirs for emerging viruses?

abstract:
  For the past 10–15 years, bats have attracted growing attention as reservoirs of emerging zoonotic viruses. This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. As bats have ancient evolutionary origins and are the only flying mammals, it has been hypothesized that some of their unique biological features may have made them especially suitable hosts for different viruses. So the question ‘Are bats different, special or exceptional?’ has become a focal point in the field of virology, bat biology and virus-host co-evolution. In this brief review, we examine the topic in a relatively unconventional way, that is, our discussion will be based on both scientific discoveries and theoretical predictions. This approach was chosen partially because the data in this field are so limited that it is impossible to conduct a useful review based on published results only and also because we believe it is important to provoke original, speculative or even controversial ideas or theories in this important field of research.


id: cord-271687-sxl8g85p
title: Chapter 8 Zoonoses in Wildlife: Integrating Ecology into Management
author: Mathews, Fiona
date: 2009-03-14
txt: ./txt/cord-271687-sxl8g85p.txt
cache: ./cache/cord-271687-sxl8g85p.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0065308X08006088
doi: 10.1016/s0065-308x(08)00608-8
summary:
  This review examines the pathways linking zoonoses in wildlife with infection in other hosts, using examples from a range of key zoonoses, including European bat lyssaviruses and bovine tuberculosis. For example, bovine tuberculosis (bTB) in the United Kingdom undoubtedly has a reservoir in wild badger populations, and the direct cost of the disease to agriculture is projected to reach £1 billion by 2011 (Department for Environment, Food and Rural Affairs (DEFRA), 2004). Examples of recent successes include the control of canine distemper virus in black-footed ferrets (Mustela nigripes) (Williams et al., 1988) , and rabies in African wild dogs (Lycaon pictus) (Hofmayer et al., 2004) and Ethiopian wolves (Canis simensis) (Haydon et al., 2004) . It proposes that a shift to ecologically based control, explicitly considering the natural history of wildlife hosts and their pathogens, is crucial in minimising the risk presented to humans, domestic animals and endangered species from zoonoses.

abstract:
  Zoonoses in wildlife not only play an important ecological role, but pose significant threats to the health of humans, domestic animals and some endangered species. More than two‐thirds of emerging, or re‐emerging, infectious diseases are thought to originate in wildlife. Despite this, co‐ordinated surveillance schemes are rare, and most efforts at disease control operate at the level of crisis management. This review examines the pathways linking zoonoses in wildlife with infection in other hosts, using examples from a range of key zoonoses, including European bat lyssaviruses and bovine tuberculosis. Ecologically based control, including the management of conditions leading to spill‐overs into target host populations, is likely to be more effective and sustainable than simple reductions in wildlife populations alone.


id: cord-272009-yxjhfg7m
title: Evolutionary Relationships between Bat Coronaviruses and Their Hosts
author: Cui, Jie
date: 2007-10-17
txt: ./txt/cord-272009-yxjhfg7m.txt
cache: ./cache/cord-272009-yxjhfg7m.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18258002/
doi: 10.3201/eid1310.070448
summary:
  Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during [2002] [2003] . Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during [2002] [2003] . Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group.

abstract:
  Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during 2002–2003. We examined the evolutionary relationships between bat CoVs and their hosts by using sequence data of the virus RNA-dependent RNA polymerase gene and the bat cytochrome b gene. Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. These shifts may be due to either virus biologic traits or host behavioral traits. This finding has implications for the emergence of SARS and for the potential future emergence of SARS-CoVs or related viruses.


id: cord-272250-asuxx1ln
title: Rabies-Related Knowledge and Practices Among Persons At Risk of Bat Exposures in Thailand
author: Robertson, Kis
date: 2011-06-28
txt: ./txt/cord-272250-asuxx1ln.txt
cache: ./cache/cord-272250-asuxx1ln.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21738801/
doi: 10.1371/journal.pntd.0001054
summary:
  CONCLUSIONS: These findings indicate the need for educational outreach to raise awareness of bat rabies, promote exposure prevention, and ensure appropriate health-seeking behaviors for bat-inflicted wounds, particularly among at-risk groups in Thailand. These findings indicate a need for educational outreach in Thailand to raise awareness of bat rabies, promote exposure prevention, and ensure health-seeking behaviors for bat-inflicted wounds, particularly among atrisk groups. Data were collected on demographics; primary bat-associated activity and years of experience; history of rabies vaccination; and type and frequency of bat exposures such as cave entry, direct contact with bats, bites and scratches from bats, and bat consumption. Individuals who reported receiving rabies vaccination were asked to indicate whether it was in direct response to an animal exposure (i.e. PEP) or for pre-exposure immunization (PreP), which is a vaccination series most often administered to people who have a relatively high likelihood of rabies virus exposure due to occupational risks or other factors.

abstract:
  BACKGROUND: Rabies is a fatal encephalitis caused by lyssaviruses. Evidence of lyssavirus circulation has recently emerged in Southeast Asian bats. A cross-sectional study was conducted in Thailand to assess rabies-related knowledge and practices among persons regularly exposed to bats and bat habitats. The objectives were to identify deficiencies in rabies awareness, describe the occurrence of bat exposures, and explore factors associated with transdermal bat exposures. METHODS: A survey was administered to a convenience sample of adult guano miners, bat hunters, game wardens, and residents/personnel at Buddhist temples where mass bat roosting occurs. The questionnaire elicited information on demographics, experience with bat exposures, and rabies knowledge. Participants were also asked to describe actions they would take in response to a bat bite as well as actions for a bite from a potentially rabid animal. Bivariate analysis was used to compare responses between groups and multivariable logistic regression was used to explore factors independently associated with being bitten or scratched by a bat. FINDINGS: Of 106 people interviewed, 11 (10%) identified bats as a potential source of rabies. A history of a bat bite or scratch was reported by 29 (27%), and 38 (36%) stated either that they would do nothing or that they did not know what they would do in response to a bat bite. Guano miners were less likely than other groups to indicate animal bites as a mechanism of rabies transmission (68% vs. 90%, p = 0.03) and were less likely to say they would respond appropriately to a bat bite or scratch (61% vs. 27%, p = 0.003). Guano mining, bat hunting, and being in a bat cave or roost area more than 5 times a year were associated with history of a bat bite or scratch. CONCLUSIONS: These findings indicate the need for educational outreach to raise awareness of bat rabies, promote exposure prevention, and ensure appropriate health-seeking behaviors for bat-inflicted wounds, particularly among at-risk groups in Thailand.


id: cord-274241-biqbsggu
title: Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis)
author: Shaw, Timothy I.
date: 2012-11-15
txt: ./txt/cord-274241-biqbsggu.txt
cache: ./cache/cord-274241-biqbsggu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23166587/
doi: 10.1371/journal.pone.0048472
summary:
  Annotated genes are involved in a broad range of activities ranging from cellular metabolism to genome regulation through ncRNAs. Reciprocal BLAST best hits yielded 8,785 sequences that are orthologous to mouse, rat, cattle, horse and human. Species tree analysis of sequences from 2,378 loci was used to achieve 95% bootstrap support for the placement of bat as sister to the clade containing horse, dog, and cattle. Through substitution rate estimation between bat and human, 32 genes were identified with evidence for positive selection. To address some of these deficiencies, we have performed transcriptome sequencing and analysis of spleen, lung, kidney and poly-IC-stimulated primary kidney cells to identify genes of interest for assessing the host response to TCRV infection. There were 20,145 contigs that mapped to Pteropus alecto, Australian flying fruit bat, and 18,359 that overlapped between genomic and transcriptome sequences for all three datasets ( Figure 5 ).

abstract:
  The Jamaican fruit bat (Artibeus jamaicensis) is one of the most common bats in the tropical Americas. It is thought to be a potential reservoir host of Tacaribe virus, an arenavirus closely related to the South American hemorrhagic fever viruses. We performed transcriptome sequencing and annotation from lung, kidney and spleen tissues using 454 and Illumina platforms to develop this species as an animal model. More than 100,000 contigs were assembled, with 25,000 genes that were functionally annotated. Of the remaining unannotated contigs, 80% were found within bat genomes or transcriptomes. Annotated genes are involved in a broad range of activities ranging from cellular metabolism to genome regulation through ncRNAs. Reciprocal BLAST best hits yielded 8,785 sequences that are orthologous to mouse, rat, cattle, horse and human. Species tree analysis of sequences from 2,378 loci was used to achieve 95% bootstrap support for the placement of bat as sister to the clade containing horse, dog, and cattle. Through substitution rate estimation between bat and human, 32 genes were identified with evidence for positive selection. We also identified 466 immune-related genes, which may be useful for studying Tacaribe virus infection of this species. The Jamaican fruit bat transcriptome dataset is a resource that should provide additional candidate markers for studying bat evolution and ecology, and tools for analysis of the host response and pathology of disease.


id: cord-274620-6ebl319q
title: Novel Lyssavirus in Bat, Spain
author: Ceballos, Nidia Aréchiga
date: 2013-05-17
txt: ./txt/cord-274620-6ebl319q.txt
cache: ./cache/cord-274620-6ebl319q.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3201/eid1905.121071
doi: 10.3201/eid1905.121071
summary:
  A new tentative lyssavirus, Lleida bat lyssavirus, was found in a bent-winged bat (Miniopterus schreibersii) in Spain. It does not belong to phylogroups I or II, and it seems to be more closely related to the West Causasian bat virus, and especially to the Ikoma lyssavirus. According to a recent phylogenetic reconstruction that included the novel IKOV and was based on a fragment of 405 nt from the nucleoprotein gene, IKOV has proven to be highly divergent (3) and probably also forms part of phylogroup III. These results suggest that this sequence tentatively belongs to a new Lyssavirus species named after the location of collection, Lleida bat lyssavirus (LLEBV). The lyssavirus-specific antigen reactivity and association with a genomic sequence found in a bent-winged bat in northeastern Spain could be derived from the tentative new virus LLEBV. schreibersii bats, as was WCBV, the other European lyssavirus outside phylogroup I.

abstract:
  A new tentative lyssavirus, Lleida bat lyssavirus, was found in a bent-winged bat (Miniopterus schreibersii) in Spain. It does not belong to phylogroups I or II, and it seems to be more closely related to the West Causasian bat virus, and especially to the Ikoma lyssavirus.


id: cord-276052-gk6n8slx
title: Isolation of Tioman virus from Pteropus giganteus bat in North-East region of India
author: Yadav, Pragya
date: 2016-09-09
txt: ./txt/cord-276052-gk6n8slx.txt
cache: ./cache/cord-276052-gk6n8slx.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134816303926
doi: 10.1016/j.meegid.2016.09.010
summary:
  During the survey for Nipah virus among bats at North-East region of India; Tioman virus (TioV), a new member of the Paramyxoviridae family was isolated from tissues of Pteropus giganteus bats for the first time in India. While investigating NiV in urine samples of giant fruit bats of the Pteropus genus on Tioman Island, Malaysia, in 2001, researchers isolated a novel virus which was placed in the Rubulavirus genus of the Paramyxoviridae family. In order to study susceptibility of different vertebrate cells to TioV, the infectious virus titer was determined by estimating 50% tissue culture infective dose (TCID 50 ) using Reed and Muench method (Reed and Muench, 1938) . Negative contrast electron microscopy of the cell supernatant of Vero CCL-81 infected with virus isolate showed the presence of virus particles with the typical paramyxovirus morphology. TioV isolated from kidney tissue homogenate of bat showed a titer of 10 4.61 /100 μL by TCID 50 in Vero CCL-81 cell line.

abstract:
  Bat-borne viral diseases are a major public health concern among newly emerging infectious diseases which includes severe acute respiratory syndrome, Nipah, Marburg and Ebola virus disease. During the survey for Nipah virus among bats at North-East region of India; Tioman virus (TioV), a new member of the Paramyxoviridae family was isolated from tissues of Pteropus giganteus bats for the first time in India. This isolate was identified and confirmed by RT-PCR, sequence analysis and electron microscopy. A range of vertebrate cell lines were shown to be susceptible to Tioman virus. Negative electron microscopy study revealed the “herringbone” morphology of the nucleocapsid filaments and enveloped particles with distinct envelope projections a characteristic of the Paramyxoviridae family. Sequence analysis of Nucleocapsid gene of TioV demonstrated sequence identity of 99.87% and 99.99% nucleotide and amino acid respectively with of TioV strain isolated in Malaysia, 2001. This report demonstrates the first isolation of Tioman virus from a region where Nipah virus activity has been noticed in the past and recent years. Bat-borne viruses have become serious concern world-wide. A Survey of bats for novel viruses in this region would help in recognizing emerging viruses and combating diseases caused by them.


id: cord-277039-yo5ojr0s
title: Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan
author: Mendenhall, Ian H.
date: 2019-04-17
txt: ./txt/cord-277039-yo5ojr0s.txt
cache: ./cache/cord-277039-yo5ojr0s.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v11040356
doi: 10.3390/v11040356
summary:
  In this study, bat guano was collected from bat caves in three different sites of southern Kazakhstan that tested positive for coronaviruses. The zoonotic SARS-coronavirus (SARS-CoV) outbreak originated in southern China from horseshoe bats, where wet markets permitted atypical contact between species, including subsequent spillover to humans [9] . On the other hand, camels are the putative natural reservoir for MERS-coronavirus, although recent phylogenetic analysis indicated that bats harbor coronaviruses that are ancestral to the MERS-CoV lineage [11] . In this study, we collected fresh bat guano from three caves at different locations in Kazakhstan and conducted molecular screening for coronaviruses. To further understand the evolutionary relationships of these viruses, we analyzed novel bat coronavirus sequences in combination with 2811 RdRp sequences of coronavirus from different host species worldwide, representing the three genera: Alpha-, Beta-, and Gamma-coronaviruses. The Alpha-CoV genus comprises a large number of coronaviruses from diverse hosts, including bats, shrews, dogs, cats, ferrets, pigs, and humans.

abstract:
  Coronaviruses are positive-stranded RNA viruses that infect a variety of hosts, resulting in a range of symptoms from gastrointestinal illness to respiratory distress. Bats are reservoirs for a high diversity of coronaviruses, and focused surveillance detected several strains genetically similar to MERS-coronavirus, SARS-coronavirus, and the human coronaviruses 229E and NL63. The bat fauna of central Asia, which link China to eastern Europe, are relatively less studied than other regions of the world. Kazakhstan is the world’s ninth largest country; however, little is understood about the prevalence and diversity of bat-borne viruses. In this study, bat guano was collected from bat caves in three different sites of southern Kazakhstan that tested positive for coronaviruses. Our phylogenetic reconstruction indicates these are novel bat coronaviruses that belong to the genus Alphacoronavirus. In addition, two distinct lineages of Kazakhstan bat coronaviruses were detected. Both lineages are closely related to bat coronaviruses from China, France, Spain, and South Africa, suggesting that co-circulation of coronaviruses is common in multiple bat species with overlapping geographical distributions. Our study highlights the need for collaborative efforts in understudied countries to increase integrated surveillance capabilities toward better monitoring and detection of infectious diseases.


id: cord-277306-r8jki3x4
author: Osborne, Christina
date: 2011-05-12
txt: ./txt/cord-277306-r8jki3x4.txt
cache: ./cache/cord-277306-r8jki3x4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.pone.0019156
doi: 10.1371/journal.pone.0019156
summary:
  At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. To increase the sensitivity of RNA detection, based on our previously published bat CoV sequences [17] and new data from this study, we designed specific primers within the amplicons of alphacoronaviruses from bats of several species in the genus Myotis and big brown bats (Table S1 ). Although the number of big brown bats sampled at site #5 was small (4 in 2008 and 14 in 2009), the prevalence of CoV RNA in these bats during these two summers was high (29% to 100%) ( Table 2) .

title:
  Alphacoronaviruses in New World Bats: Prevalence, Persistence, Phylogeny, and Potential for Interaction with Humans

abstract:
  Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.


id: cord-277309-kelebqr6
title: Viruses in bats and potential spillover to animals and humans
author: Wang, Lin-Fa
date: 2019-01-18
txt: ./txt/cord-277309-kelebqr6.txt
cache: ./cache/cord-277309-kelebqr6.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S187962571830107X
doi: 10.1016/j.coviro.2018.12.007
summary:
  While it is not easy to assess the spillover potential of many SARS-CoV related bat CoVs due to unsuccessful attempts to isolate the viruses, it should be noted that a ''consensus'' virus constructed via reverse genetics pointed to a high probability of human infection [19] . Further study is required to determine the true zoonotic potential of SADS-CoV and closely related bat CoVs. For unknown reasons, despite of the wide presence of CoVs in bats of different locations and species with relative high viral genome levels, multiple attempts by different international groups to isolate bat CoVs have been largely unsuccessful. The genetic and functional Viruses in bats and potential spillover to animals and humans Wang and Anderson 81 Aside from MenPV and TioPV, other paramyxoviruses from the genus Rubulavirus have been isolated from or detected in bats without evidence of zoonotic transmission.

abstract:
  In the last two decades, several high impact zoonotic disease outbreaks have been linked to bat-borne viruses. These include SARS coronavirus, Hendra virus and Nipah virus. In addition, it has been suspected that ebolaviruses and MERS coronavirus are also linked to bats. It is being increasingly accepted that bats are potential reservoirs of a large number of known and unknown viruses, many of which could spillover into animal and human populations. However, our knowledge into basic bat biology and immunology is very limited and we have little understanding of major factors contributing to the risk of bat virus spillover events. Here we provide a brief review of the latest findings in bat viruses and their potential risk of cross-species transmission.


id: cord-281956-obwtd33y
title: Pathogenic Leptospira spp. in bats: Molecular investigation in Southern Brazil
author: Mayer, Fabiana Quoos
date: 2017-05-12
txt: ./txt/cord-281956-obwtd33y.txt
cache: ./cache/cord-281956-obwtd33y.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S014795711730036X
doi: 10.1016/j.cimid.2017.05.003
summary:
  isolation, leptospiral carriage was demonstrated in bats of different species from southern Brazil, which reinforces the need for surveillance of infectious agents in wild animals. Despite this wide range of bat species and high rates of leptospirosis, there are few Brazilian studies on this subject showing low bat leptospiral infection rates [4, 18] ; however, they were performed in urban areas of Southeast region. Thus, in the present study, we sought to investigate the frequency of pathogenic Leptospira strains in bats from different areas of Rio Grande do Sul, the southern Brazilian state, which has a different ecosystem. In the present study, there was no association among age (p = 0.502), sex (p = 0.867), species (p = 0.139), season of collection (p = 0.838), location (p = 0.477), feeding habits (p = 1.000) or family (p = 0.09) and the frequency of positive results for pathogenic Leptospira.

abstract:
  The present study aimed to investigate the frequency of pathogenic Leptospira spp. in Brazilian bats and to determine possible risk factors associated to it. Ninety two bats of 12 species were evaluated. Whole genomic DNA from kidneys was extracted and real-time PCR specific to pathogenic Leptospira spp. was applied. Association between the frequency of specimens positive for Leptospira spp. and sex, age, bat species or family, season of collection, geographic localization and feeding habits was evaluated. The results showed that 39.13% of analyzed bats were found positive for Leptospira spp. Nine bat species had at least one positive result. There was no association among the evaluated variables and frequency of pathogenic Leptospira spp. Although the limitations due to lack of Leptospira spp. isolation, leptospiral carriage was demonstrated in bats of different species from southern Brazil, which reinforces the need for surveillance of infectious agents in wild animals.


id: cord-283756-ycjzitlk
title: Potential for Introduction of Bat-Borne Zoonotic Viruses into the EU: A Review
author: Simons, Robin R. L.
date: 2014-05-16
txt: ./txt/cord-283756-ycjzitlk.txt
cache: ./cache/cord-283756-ycjzitlk.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v6052084
doi: 10.3390/v6052084
summary:
  Bat-borne viruses can pose a serious threat to human health, with examples including Nipah virus (NiV) in Bangladesh and Malaysia, and Marburg virus (MARV) in Africa. In assessing the risks of introduction of these bat-borne zoonotic viruses to the EU, it is important to consider the location and range of bat species known to be susceptible to infection, together with the virus prevalence, seasonality of viral pulses, duration of infection and titre of virus in different bat tissues. Bats are known to have varying degrees of contact with domestic animals and commercial food crops [20, 21] , in particular contact of Pteropus giganteus bats with date palm sap producing trees in Bangladesh is considered a risk factor for human NiV infection [22] . It can be seen that while recent human infections of both NiV and MARV appear to be limited in geographical range (the red areas in Figure 2 ), there are a number of countries where bats have been identified as having the virus, but no human infection has been reported.

abstract:
  Bat-borne viruses can pose a serious threat to human health, with examples including Nipah virus (NiV) in Bangladesh and Malaysia, and Marburg virus (MARV) in Africa. To date, significant human outbreaks of such viruses have not been reported in the European Union (EU). However, EU countries have strong historical links with many of the countries where NiV and MARV are present and a corresponding high volume of commercial trade and human travel, which poses a potential risk of introduction of these viruses into the EU. In assessing the risks of introduction of these bat-borne zoonotic viruses to the EU, it is important to consider the location and range of bat species known to be susceptible to infection, together with the virus prevalence, seasonality of viral pulses, duration of infection and titre of virus in different bat tissues. In this paper, we review the current scientific knowledge of all these factors, in relation to the introduction of NiV and MARV into the EU.


id: cord-284015-vvtv492b
title: Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera
author: Nikaido, Masato
date: 2020-09-23
txt: ./txt/cord-284015-vvtv492b.txt
cache: ./cache/cord-284015-vvtv492b.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32966557/
doi: 10.1093/dnares/dsaa021
summary:
  We identified that megabat genomes are distinct in that they have extremely low activity of SINE retrotranspositions, expansion of two chemosensory gene families, including the trace amine receptor (TAAR) and olfactory receptor (OR), and elevation of the dN/dS ratio in genes for immunity and protein catabolism. The protein-coding genes in the genomes of Egyptian fruit bat and Leschenault''s rousette were identified based on the alignment with annotated gene sequences of 14 mammals (cat, dog, horse, cow, hedgehog, human, macaque, mouse, rat, Black flying fox, Little brown bat, Brandt''s bat, David''s myotis, and Large flying fox; Supplementary Table S2 ) that are available in the database. 71 Suggesting that FPR-mediated chemodetection is not directly linked with the difference in their habitats, mega-and microbats both possess two to eight FPRs. However, a previous study, by comparing the orthologous sequences among a broad range of mammals, found the signatures for the operation of positive selection in FPRs. 72 Therefore, to examine the possible contribution of FPRs to the adaptive evolution of megabats, more detailed investigation is necessary by focussing on the dN/dS values among orthologous FPR sequences of many bat species, which are lacking at present.

abstract:
  The revision of the sub-order Microchiroptera is one of the most intriguing outcomes in recent mammalian molecular phylogeny. The unexpected sister–taxon relationship between rhinolophoid microbats and megabats, with the exclusion of other microbats, suggests that megabats arose in a relatively short period of time from a microbat-like ancestor. In order to understand the genetic mechanism underlying adaptive evolution in megabats, we determined the whole-genome sequences of two rousette megabats, Leschenault’s rousette (Rousettus leschenaultia) and the Egyptian fruit bat (R. aegyptiacus). The sequences were compared with those of 22 other mammals, including nine bats, available in the database. We identified that megabat genomes are distinct in that they have extremely low activity of SINE retrotranspositions, expansion of two chemosensory gene families, including the trace amine receptor (TAAR) and olfactory receptor (OR), and elevation of the dN/dS ratio in genes for immunity and protein catabolism. The adaptive signatures discovered in the genomes of megabats may provide crucial insight into their distinct evolution, including key processes such as virus resistance, loss of echolocation, and frugivorous feeding.


id: cord-284367-cy61pjcb
title: Molecular Epidemiology of Paramyxoviruses in Frugivorous Eidolon helvum Bats in Zambia
author: MULEYA, Walter
date: 2013-12-31
txt: ./txt/cord-284367-cy61pjcb.txt
cache: ./cache/cord-284367-cy61pjcb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24389743/
doi: 10.1292/jvms.13-0518
summary:
  In this study, we describe the detection of novel paramyxoviruses from the Eidolon helvum species of fruit bats. Semi-nested RT-PCR detected a total of 25 (8%) positive samples for paramyxoviruses which were then directly sequenced and analyzed using phylogenetic analysis. Our study identified novel Henipavirus-related and unrelated viruses using RT-PCR in fruit bats from Kansaka National Park and indicated the presence of similar Bat paramyxoviruses originating from wide geographic areas, suggesting the ability of bats to harbor and transmit viruses. This has been as a result of the high detection rate of previously unknown viral sequences in bats coupled with the emergence of pathogens, such as Hendra, Nipah, Severe acute respiratory syndrome (SARS)-Corona, Ebola and Marburg viruses, all of which are highly virulent and pose a great zoonotic risk [2, 3, 8, 9, 17] . The samples from Zambia formed clusters with the Henipavirus-related viruses and with the unclassified Bat paramyxoviruses (Fig. 1) .

abstract:
  In this study, we describe the detection of novel paramyxoviruses from the Eidolon helvum species of fruit bats. We extracted RNA from 312 spleen samples from bats captured in Zambia over a period of 4 years (2008–2011). Semi-nested RT-PCR detected a total of 25 (8%) positive samples for paramyxoviruses which were then directly sequenced and analyzed using phylogenetic analysis. Among the positive samples, seven novel paramyxoviruses were detected. Five viruses were closely related to the genus Henipavirus, while two viruses were related to the unclassified Bat paramyxoviruses from Ghana and Congo Brazzaville. Our study identified novel Henipavirus-related and unrelated viruses using RT-PCR in fruit bats from Kansaka National Park and indicated the presence of similar Bat paramyxoviruses originating from wide geographic areas, suggesting the ability of bats to harbor and transmit viruses. The presence of these viruses in fruit bats might pose a public health risk.


id: cord-286708-igu984oc
author: Chua, Kaw Bing
date: 2008-11-25
txt: ./txt/cord-286708-igu984oc.txt
cache: ./cache/cord-286708-igu984oc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/19030226/
doi: 10.1371/journal.pone.0003803
summary:
  Recently, our group reported the isolation of the Melaka virus from a patient with acute respiratory disease and provided data suggesting that this new orthoreovirus is capable of human-to-human transmission and is probably of bat origin. Here we report yet another Melaka-like reovirus (named Kampar virus) isolated from the throat swab of a 54 year old male patient in Kampar, Perak, Malaysia who was suffering from high fever, acute respiratory disease and vomiting at the time of virus isolation. Here, we report the discovery and characterization of Kampar virus (KamV), the fourth member in the NBV species group and its isolation from a human patient with fever and acute respiratory illness. Due to the similar CPE morphology ( Figure 1 ) and cell line susceptibility patterns between KamV and the recently discovered Melaka virus (MelV), which also causes acute respiratory diseases in humans [5] , immunofluorescent antibody testing was conducted to examine cross reactivity.

title:
  Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections

abstract:
  First discovered in the early 1950s, reoviruses (respiratory enteric orphan viruses) were not associated with any known disease, and hence named orphan viruses. Recently, our group reported the isolation of the Melaka virus from a patient with acute respiratory disease and provided data suggesting that this new orthoreovirus is capable of human-to-human transmission and is probably of bat origin. Here we report yet another Melaka-like reovirus (named Kampar virus) isolated from the throat swab of a 54 year old male patient in Kampar, Perak, Malaysia who was suffering from high fever, acute respiratory disease and vomiting at the time of virus isolation. Serological studies indicated that Kampar virus was transmitted from the index case to at least one other individual and caused respiratory disease in the contact case. Sequence analysis of the four small class genome segments indicated that Kampar and Melaka viruses are closely related. This was confirmed by virus neutralization assay, showing an effective two-way cross neutralization, i.e., the serum against one virus was able to neutralize the other. Although the exact origin of Kampar virus is unknown, epidemiological tracing revealed that the house of the index case is surrounded by fruit trees frequently visited by fruit bats. There is a high probability that Kampar virus originated from bats and was transmitted to humans via bat droppings or contaminated fruits. The discovery of Kampar virus highlights the increasing trend of emergence of bat zoonotic viruses and the need to expand our understanding of bats as a source of many unknown viruses.


id: cord-287131-svtdfeop
title: Bat Influenza A(HL18NL11) Virus in Fruit Bats, Brazil
author: Campos, Angélica Cristine Almeida
date: 2019-02-17
txt: ./txt/cord-287131-svtdfeop.txt
cache: ./cache/cord-287131-svtdfeop.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30666923/
doi: 10.3201/eid2502.181246
summary:
  Screening of 533 bats for influenza A viruses showed subtype HL18NL11 in intestines of 2 great fruit-eating bats (Artibeus lituratus). Genomic characterizations revealed conservation of viral genes across different host species, countries, and sampling years, suggesting a conserved cellular receptor and wide-ranging occurrence of bat influenza A viruses. The segmented influenza A genome facilitates reassortment events in birds or intermediate hosts, such as swine and horses, leading to emergence of new variants potentially capable of causing zoonotic infections (2) . All critical amino acid residues associated with influenza A virus replication and entry (4,5) were conserved between the Brazil and the Peru HL18NL11 strains, including the HA monobasic cleavage site motif PIKETR/GLF (5) . Phylogenetic analyses confirmed the close genetic relationship between Peru and Brazil HL18NL11 variants across all 8 segments (Figure 2 ; Appendix Table 2 ), suggesting lack of reassortment events according to the available data.

abstract:
  Screening of 533 bats for influenza A viruses showed subtype HL18NL11 in intestines of 2 great fruit-eating bats (Artibeus lituratus). High concentrations suggested fecal shedding. Genomic characterizations revealed conservation of viral genes across different host species, countries, and sampling years, suggesting a conserved cellular receptor and wide-ranging occurrence of bat influenza A viruses.


id: cord-287748-co9j3uig
title: Detection of bat hepatitis E virus RNA in microbats in Japan
author: Kobayashi, Tomoya
date: 2018-05-29
txt: ./txt/cord-287748-co9j3uig.txt
cache: ./cache/cord-287748-co9j3uig.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29845506/
doi: 10.1007/s11262-018-1577-9
summary:
  Several recent studies have reported that various bat species harbor bat hepatitis E viruses (BatHEV) belonging to the family Hepeviridae, which also contains human hepatitis E virus (HEV). Here, we collected and screened 81 bat fecal samples from nine bat species in Japan to detect BatHEV RNA by RT-PCR using HEV-specific primers, and detected three positive samples. These data support the first detection of BatHEVs in Japanese microbats, indicating their wide geographical distribution among multiple bat species. BLAST analysis indicated that BtHEV-Ej1/-Ej2 showed the highest sequence identities to BatHEV/BS7, a German strain detected from the Serotine bat (Eptesicus serotinus), among strains previously reported in other countries. The closely related BatHEVs (BtHEV-Ej1/-Ej2 and Bat HEV/BS7) have been detected in different species of Eptesicus bats (E. PCR amplifications were performed using the KOD FX Neo (Toyobo) with consensus HEV primer sets (PanHEV F and R), which were designed in this study to amplify a 191-bp fragment of the RNA-dependent into Orthohepevirus D, in Japanese bats, suggesting wide geographical distribution of BatHEV among multiple bat species.

abstract:
  Several recent studies have reported that various bat species harbor bat hepatitis E viruses (BatHEV) belonging to the family Hepeviridae, which also contains human hepatitis E virus (HEV). The distribution and ecology of BatHEV are not well known. Here, we collected and screened 81 bat fecal samples from nine bat species in Japan to detect BatHEV RNA by RT-PCR using HEV-specific primers, and detected three positive samples. Sequence and phylogenetic analyses indicated that these three viruses were BatHEVs belonging to genus Orthohepevirus D like other BatHEV strains reported earlier in various countries. These data support the first detection of BatHEVs in Japanese microbats, indicating their wide geographical distribution among multiple bat species.


id: cord-288451-npefpo3t
title: Novel highly divergent reassortant bat rotaviruses in Cameroon, without evidence of zoonosis
author: Yinda, Claude Kwe
date: 2016-09-26
txt: ./txt/cord-288451-npefpo3t.txt
cache: ./cache/cord-288451-npefpo3t.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27666390/
doi: 10.1038/srep34209
summary:
  In the current study we investigated the genetic diversity of RVAs in fecal samples from 87 straw-colored fruit bats living in close contact with humans in Cameroon using viral metagenomics. The VP6, VP2, NSP2, NSP3 and NSP5 gene segments of BatLy03 phylogenetically clustered together with the Kenyan bat RVA strain KE4852 in the previously established I15, C8, N8, T11 and H10 genotypes, respectively (Fig. 4) . In order to find out if the currently used human RVA screening primers would detect the bat RVA strain from this study in case of zoonosis, we compared these primers with their corresponding sequences in the respective gene segments (Table 2 and Supplementary data S2). Screening human samples for these bat RVAs indicated no interspecies transmissions and primer comparison showed that not all the strains can be picked up with the currently used screening primers.

abstract:
  Bats are an important reservoir for zoonotic viruses. To date, only three RVA strains have been reported in bats in Kenya and China. In the current study we investigated the genetic diversity of RVAs in fecal samples from 87 straw-colored fruit bats living in close contact with humans in Cameroon using viral metagenomics. Five (near) complete RVA genomes were obtained. A single RVA strain showed a partial relationship with the Kenyan bat RVA strain, whereas the other strains were completely novel. Only the VP7 and VP4 genes showed significant variability, indicating the occurrence of frequent reassortment events. Comparing these bat RVA strains with currently used human RVA screening primers indicated that most of the novel VP7 and VP4 segments would not be detected in routine epidemiological screening studies. Therefore, novel consensus screening primers were developed and used to screen samples from infants with gastroenteritis living in close proximity with the studied bat population. Although RVA infections were identified in 36% of the infants, there was no evidence of zoonosis. This study identified multiple novel bat RVA strains, but further epidemiological studies in humans will have to assess if these viruses have the potential to cause gastroenteritis in humans.


id: cord-289555-1z4vbldd
author: Mühldorfer, Kristin
date: 2011-12-28
txt: ./txt/cord-289555-1z4vbldd.txt
cache: ./cache/cord-289555-1z4vbldd.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/22216354/
doi: 10.1371/journal.pone.0029773
summary:
  Comparative analysis of pathological findings and microbiological results show that microbial agents indeed have an impact on bats succumbing to infectious diseases, with fatal bacterial, viral and parasitic infections found in at least 12% of the bats investigated. The clear seasonal and individual variations in disease prevalence and infection rates indicate that maternity colonies are more susceptible to infectious agents, underlining the possible important role of host physiology, immunity and roosting behavior as risk factors for infection of bats. In this study, we provide new data on infectious diseases in European bat species, considering factors likely to affect the susceptibility of bats to infectious agents including effects of seasonality, individual and species-specific heterogeneities, and possible intra-and inter-species transmission dynamics. Comparative bacteriologic and histo-pathologic analysis identified 22 different bacterial species that were clearly associated with pathological lesions and/or systemic infection, found in 17% (n = 73) of bats investigated bacteriologically ( Table 5) .

title:
  Diseases and Causes of Death in European Bats: Dynamics in Disease Susceptibility and Infection Rates

abstract:
  BACKGROUND: Bats receive increasing attention in infectious disease studies, because of their well recognized status as reservoir species for various infectious agents. This is even more important, as bats with their capability of long distance dispersal and complex social structures are unique in the way microbes could be spread by these mammalian species. Nevertheless, infection studies in bats are predominantly limited to the identification of specific pathogens presenting a potential health threat to humans. But the impact of infectious agents on the individual host and their importance on bat mortality is largely unknown and has been neglected in most studies published to date. METHODOLOGY/PRINCIPAL FINDINGS: Between 2002 and 2009, 486 deceased bats of 19 European species (family Vespertilionidae) were collected in different geographic regions in Germany. Most animals represented individual cases that have been incidentally found close to roosting sites or near human habitation in urban and urban-like environments. The bat carcasses were subjected to a post-mortem examination and investigated histo-pathologically, bacteriologically and virologically. Trauma and disease represented the most important causes of death in these bats. Comparative analysis of pathological findings and microbiological results show that microbial agents indeed have an impact on bats succumbing to infectious diseases, with fatal bacterial, viral and parasitic infections found in at least 12% of the bats investigated. CONCLUSIONS/SIGNIFICANCE: Our data demonstrate the importance of diseases and infectious agents as cause of death in European bat species. The clear seasonal and individual variations in disease prevalence and infection rates indicate that maternity colonies are more susceptible to infectious agents, underlining the possible important role of host physiology, immunity and roosting behavior as risk factors for infection of bats.


id: cord-289584-rbp7p8s9
author: Zhou, Ling
date: 2019-01-09
txt: ./txt/cord-289584-rbp7p8s9.txt
cache: ./cache/cord-289584-rbp7p8s9.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30171801/
doi: 10.1111/tbed.13008
summary:
  So far, six coronaviruses have been identified from pigs, which include porcine epidemic diarrhoea virus (PEDV), porcine respiratory coronavirus (PRCV), SADS-CoV and transmissible gastroenteritis virus (TGEV) that all belong to the Alphacoronavirus genus, as well as one betacoronavirus, porcine hemagglutinating encephalomyelitis virus (PHEV) and one deltacoronavirus, porcine deltacoronavirus (PDCoV) (Lin, Saif, Marthaler, & Wang, 2016; Wesley, Woods, & Cheung, 1991; Woo et al., 2010) . Our results also indicated that both the complete genomes, N genes and S genes of all SADS-CoV strains shared the highest nucleotides identifies with those corresponding sequences of four bat coronavirus HKU2 strains. In this work, The phylogenetic trees of full length genomes and S genes of SADS-CoV sequences showed that the SADS-CoV branch clustered with these four HKU2 strains, which is same to previous results (Gong et al., 2017; Pan et al., 2017; Zhou et al., 2018) .

title:
  Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China

abstract:
  Swine acute diarrhoea syndrome coronavirus (SADS‐CoV), a novel coronavirus, was first discovered in southern China in January 2017 and caused a large scale outbreak of fatal diarrheal disease in piglets. Here, we conducted a retrospective investigation of 236 samples from 45 swine farms with a clinical history of diarrheal disease to evaluate the emergence and the distribution of SADS‐CoV in pigs in China. Our results suggest that SADS‐CoV has emerged in China at least since August 2016. Meanwhile, we detected a prevalence of SADS‐CoV (43.53%), porcine deltacoronavirus (8.83%), porcine epidemic diarrhoea virus (PEDV) (78.25%), rotavirus (21.77%), and transmissible gastroenteritis virus (0%), and we also found the co‐infection of SADS‐CoV and PEDV occurred most frequently with the rate of 17.65%. We screened and obtained two new complete genomes, five N and five S genes of SADS‐CoV. Phylogenetic analysis based on these sequences revealed that all SADS‐CoV sequences in this study clustered with previously reported SADS‐CoV strains to form a well defined branch that grouped with the bat coronavirus HKU2 strains. This study is the first retrospective investigation for SADS‐CoV and provides the epidemiological information of this new virus in China, which highlights the urgency to develop effective measures to control SADS‐CoV.


id: cord-291965-9r9ll83m
author: Pfefferle, Susanne
date: 2009-09-17
txt: ./txt/cord-291965-9r9ll83m.txt
cache: ./cache/cord-291965-9r9ll83m.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/19788804/
doi: 10.3201/eid1509.090224
summary:
  Studies conducted in China in the aftermath of the SARS epidemic have identified CoVs in bats (Chiroptera) and implicated this speciose mammalian order as the most likely reservoir of all known coronaviruses (3) (4) (5) (6) (7) . Bayesian phylogenetic inference with different substitution models and parallel analysis using Metropolis coupling now placed the virus reliably next to a common ancestor with the 2b group of CoV (SARS-like viruses, Figure 3 ). These fragments could be combined into contig*MRCA, most recent common ancestor; CI, confidence interval; HPD, high population density; SARS, severe acute respiratory syndrome; hCoV, human coronavirus; GTR + + I, general time reversible gamma-shaped rate distribution across sites and an invariant site assumption. One of our Hipposideros CoVs was in a basal phylogenetic relationship with the SARS-like clade (group 2b); their most recent common ancestors date back to ≈400 bc.

title:
  Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana

abstract:
  We tested 12 bat species in Ghana for coronavirus (CoV) RNA. The virus prevalence in insectivorous bats (n = 123) was 9.76%. CoV was not detected in 212 fecal samples from Eidolon helvum fruit bats. Leaf-nosed bats pertaining to Hipposideros ruber by morphology had group 1 and group 2 CoVs. Virus concentrations were <45,000 copies/100 mg of bat feces. The diversified group 1 CoV shared a common ancestor with the human common cold virus hCoV-229E but not with hCoV-NL63, disputing hypotheses of common human descent. The most recent common ancestor of hCoV-229E and GhanaBt-CoVGrp1 existed in ≈1686–1800 ad. The GhanaBt-CoVGrp2 shared an old ancestor (≈2,400 years) with the severe acute respiratory syndrome–like group of CoV.


id: cord-293946-4bquxdqa
author: Huong, Nguyen Quynh
date: 2020-08-10
txt: ./txt/cord-293946-4bquxdqa.txt
cache: ./cache/cord-293946-4bquxdqa.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32776964/
doi: 10.1371/journal.pone.0237129
summary:
  In this study we investigated the presence and diversity of coronavirus sequences in the field rat trade distribution chain, wildlife farms specializing in raising rodents for human consumption, and bat guano "farms" and roosts near human dwellings to better understand the natural hosts of coronaviruses and the risk for these interfaces to facilitate spillover into humans. Out of 70 sites, coronavirus positives were detected at 58 including 100% (24/24) of live rat trade sites, 60.7% (17/28) of rodent wildlife farm sites, 94.1% (16/17) of bat guano farm sites, and at the one natural pteropid bat roost. Significant findings of this study are the high proportion of coronavirus positive wildlife (bats and rodents) and the increasing proportion of positives found along the rat trade supply chain from sub-interfaces close to the capture site (rat traders) to restaurants.

title:
  Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014

abstract:
  Outbreaks of emerging coronaviruses in the past two decades and the current pandemic of a novel coronavirus (SARS-CoV-2) that emerged in China highlight the importance of this viral family as a zoonotic public health threat. To gain a better understanding of coronavirus presence and diversity in wildlife at wildlife-human interfaces in three southern provinces in Viet Nam 2013–2014, we used consensus Polymerase Chain Reactions to detect coronavirus sequences. In comparison to previous studies, we observed high proportions of positive samples among field rats (34.0%, 239/702) destined for human consumption and insectivorous bats in guano farms (74.8%, 234/313) adjacent to human dwellings. Most notably among field rats, the odds of coronavirus RNA detection significantly increased along the supply chain from field rats sold by traders (reference group; 20.7% positivity, 39/188) by a factor of 2.2 for field rats sold in large markets (32.0%, 116/363) and 10.0 for field rats sold and served in restaurants (55.6%, 84/151). Coronaviruses were also detected in rodents on the majority of wildlife farms sampled (60.7%, 17/28). These coronaviruses were found in the Malayan porcupines (6.0%, 20/331) and bamboo rats (6.3%, 6/96) that are raised on wildlife farms for human consumption as food. We identified six known coronaviruses in bats and rodents, clustered in three Coronaviridae genera, including the Alpha-, Beta-, and Gammacoronaviruses. Our analysis also suggested either mixing of animal excreta in the environment or interspecies transmission of coronaviruses, as both bat and avian coronaviruses were detected in rodent feces on wildlife farms. The mixing of multiple coronaviruses, and their apparent amplification along the wildlife supply chain into restaurants, suggests maximal risk for end consumers and likely underpins the mechanisms of zoonotic spillover to people.


id: cord-294698-mtfrbn87
author: Kim, H. K.
date: 2016-05-23
txt: ./txt/cord-294698-mtfrbn87.txt
cache: ./cache/cord-294698-mtfrbn87.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/tbed.12515
doi: 10.1111/tbed.12515
summary:
  In this study, consensus primer‐based reverse transcriptase polymerase chain reactions (RT‐PCRs) and high‐throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Therefore, in this study, we investigated viruses in bat species in Korea, using 49 faecal samples collected from July to December 2015 in 11 sites in natural bat habitats. So far, group H rotaviruses have only been reported in human and pigs (Molinari et al., 2015) , but this study provides evidence that bat species may be a host of group H RVs. To confirm that, there should be follow-up studies including virus isolation and characterization, genomic analysis, continuous surveillance and VP6-based classification (Matthijnssens et al., 2012) to find its prevalence, epidemiology and zoonotic potential. In this study, SARS-CoV-like and MERS-CoV-like bat CoVs and group H rotavirus were detected for this first time in Korea, which may be of interest because of their zoonosis potential.

title:
  Detection of Severe Acute Respiratory Syndrome‐Like, Middle East Respiratory Syndrome‐Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats

abstract:
  Bat species around the world have recently been recognized as major reservoirs of several zoonotic viruses, such as severe acute respiratory syndrome coronavirus (SARS‐CoV), Middle East respiratory syndrome coronavirus (MERS‐CoV), Nipah virus and Hendra virus. In this study, consensus primer‐based reverse transcriptase polymerase chain reactions (RT‐PCRs) and high‐throughput sequencing were performed to investigate viruses in bat faecal samples collected at 11 natural bat habitat sites from July to December 2015 in Korea. Diverse coronaviruses were first detected in Korean bat faeces, including alphacoronaviruses, SARS‐CoV‐like and MERS‐CoV‐like betacoronaviruses. In addition, we identified a novel bat rotavirus belonging to group H rotavirus which has only been described in human and pigs until now. Therefore, our results suggest the need for continuing surveillance and additional virological studies in domestic bat.


id: cord-295433-olmein3q
title: Bats and Coronaviruses
author: Banerjee, Arinjay
date: 2019-01-09
txt: ./txt/cord-295433-olmein3q.txt
cache: ./cache/cord-295433-olmein3q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30634396/
doi: 10.3390/v11010041
summary:
  Initial studies investigating animal sources of the virus from "wet markets" in the Guangdong province of China suggested that Himalayan palm civets and raccoon dogs were the most likely hosts responsible for human transmission [22] ; however, the role of bats as the original animal reservoir hosts of SARS-CoV was speculated as similar viruses were detected in them [27, 28] . A recent study found that 16 out of 30 camel workers surveyed in Saudi Arabia show evidence of prior MERS-CoV infection via seroconversion and/or virus-specific CD8+ T cell responses without any history of significant respiratory disease. The primary bat species being used to study the bat immune response to virus infections in vitro and in vivo are Pteropus alecto (black flying fox), Rousettus aegyptiacus (Egyptian rousette), and Artibeus jamaicensis (Jamaican fruit bat). Multiple studies with PEDV, SARS-and MERS-CoVs have identified accessory proteins that can effectively inhibit an IFN response in mammalian cells [12] [13] [14] [91] [92] [93] [94] [95] .

abstract:
  Bats are speculated to be reservoirs of several emerging viruses including coronaviruses (CoVs) that cause serious disease in humans and agricultural animals. These include CoVs that cause severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), porcine epidemic diarrhea (PED) and severe acute diarrhea syndrome (SADS). Bats that are naturally infected or experimentally infected do not demonstrate clinical signs of disease. These observations have allowed researchers to speculate that bats are the likely reservoirs or ancestral hosts for several CoVs. In this review, we follow the CoV outbreaks that are speculated to have originated in bats. We review studies that have allowed researchers to identify unique adaptation in bats that may allow them to harbor CoVs without severe disease. We speculate about future studies that are critical to identify how bats can harbor multiple strains of CoVs and factors that enable these viruses to “jump” from bats to other mammals. We hope that this review will enable readers to identify gaps in knowledge that currently exist and initiate a dialogue amongst bat researchers to share resources to overcome present limitations.


id: cord-295554-0pzjyrdf
author: Lima, Francisco Esmaile de Sales
date: 2013-03-16
txt: ./txt/cord-295554-0pzjyrdf.txt
cache: ./cache/cord-295554-0pzjyrdf.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23504146/
doi: 10.1007/s11262-013-0899-x
summary:
  A variety of other coronaviruses have been detected in many bat species from Asia, including specimens of the genus Rhinolophus, which were found to be infected with SARS-like CoV. In view of the potential role that bats may play in the transmission of new viral infections to humans and other species, this study was set up in search for coronavirus genomes in bats from the urban area of Porto Alegre (30°01 0 59 00 S; 51°13 0 48 00 W), a town with about 1.5 million inhabitants and capital of the state of Rio Grande do Sul, Brazil. In our study, we detected RdRp sequences of bat CoV at a frequency of 19.33 % in the examined samples; such frequency is comparable to previous results obtained in similar studies from different bat species in other countries (ranging figure) .

title:
  Detection of Alphacoronavirus in velvety free-tailed bats (Molossus molossus) and Brazilian free-tailed bats (Tadarida brasiliensis) from urban area of Southern Brazil

abstract:
  A survey was carried out in search for bat coronaviruses in an urban maternity roost of about 500 specimens of two species of insectivorous bats, Molossus molossus and Tadarida brasiliensis, in Southern Brazil. Twenty-nine out of 150 pooled fecal samples tested positive by reverse transcription-PCR contained fragments of the RNA-dependent RNA polymerase gene of coronavirus-related viruses. The sequences clustered along with bat alphacoronaviruses, forming a subcluster within this group. Our findings point to the need for risk assessment and continued surveillance of coronavirus infections of bats in Brazil. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-013-0899-x) contains supplementary material, which is available to authorized users.


id: cord-295727-s63lffi8
author: Lima, Luciana
date: 2013-08-03
txt: ./txt/cord-295727-s63lffi8.txt
cache: ./cache/cord-295727-s63lffi8.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1756-3305-6-221
doi: 10.1186/1756-3305-6-221
summary:
  Barcoding, phylogenetic analyses and genetic distances based on SSU rRNA and gGAPDH supported these trypanosomes as a new species, which we named Trypanosoma livingstonei n. In this study, we isolated and characterised 14 new trypanosomes from African bats captured in Mozambique, southeast Africa, by inferring phylogenetic relationships using ribosomal SSU rRNA, gGAPDH and SL genes. In this study, barcoding using V7V8 SSU rRNA revealed that all new isolates from African bats shared high sequence similarity; 2-3 cloned sequences were determined for each isolate, and they tightly clustered together and were virtually identical (~0.2% of divergence) and different from any previously reported trypanosome species. Here, the new bat isolates were initially positioned using independent gGAPDH ( Figure 3 ) and SSU rRNA (data not shown) sequences in phylogenetic trees comprising representative species of all major trypanosome clades. In all phylogenetic trees, the new bat isolates formed a well-supported clade close to Australian trypanosomes (10% divergence) and basal to the T.

title:
  Trypanosoma livingstonei: a new species from African bats supports the bat seeding hypothesis for the Trypanosoma cruzi clade

abstract:
  BACKGROUND: Bat trypanosomes have been implicated in the evolutionary history of the T. cruzi clade, which comprises species from a wide geographic and host range in South America, Africa and Europe, including bat-restricted species and the generalist agents of human American trypanosomosis T. cruzi and T. rangeli. METHODS: Trypanosomes from bats (Rhinolophus landeri and Hipposideros caffer) captured in Mozambique, southeast Africa, were isolated by hemoculture. Barcoding was carried out through the V7V8 region of Small Subunit (SSU) rRNA and Fluorescent Fragment Length barcoding (FFLB). Phylogenetic inferences were based on SSU rRNA, glyceraldehyde phosphate dehydrogenase (gGAPDH) and Spliced Leader (SL) genes. Morphological characterization included light, scanning and transmission electron microscopy. RESULTS: New trypanosomes from bats clustered together forming a clade basal to a larger assemblage called the T. cruzi clade. Barcoding, phylogenetic analyses and genetic distances based on SSU rRNA and gGAPDH supported these trypanosomes as a new species, which we named Trypanosoma livingstonei n. sp. The large and highly polymorphic SL gene repeats of this species showed a copy of the 5S ribosomal RNA into the intergenic region. Unique morphological (large and broad blood trypomastigotes compatible to species of the subgenus Megatrypanum and cultures showing highly pleomorphic epimastigotes and long and slender trypomastigotes) and ultrastructural (cytostome and reservosomes) features and growth behaviour (when co-cultivated with HeLa cells at 37°C differentiated into trypomastigotes resembling the blood forms and do not invaded the cells) complemented the description of this species. CONCLUSION: Phylogenetic inferences supported the hypothesis that Trypanosoma livingstonei n. sp. diverged from a common ancestral bat trypanosome that evolved exclusively in Chiroptera or switched at independent opportunities to mammals of several orders forming the clade T. cruzi, hence, providing further support for the bat seeding hypothesis to explain the origin of T. cruzi and T. rangeli.


id: cord-297790-tpjxt0w5
title: Going to Bat(s) for Studies of Disease Tolerance
author: Mandl, Judith N.
date: 2018-09-20
txt: ./txt/cord-297790-tpjxt0w5.txt
cache: ./cache/cord-297790-tpjxt0w5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3389/fimmu.2018.02112
doi: 10.3389/fimmu.2018.02112
summary:
  Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. It is likely that differences in evolutionary history of pathogen exposure between bats and humans have led to distinct adaptations in anti-viral immune responses and the ability to tolerate certain infections without disease while being susceptible to others. We summarize this work below, but comparisons of observations made across species suggest that although a number of species appear to be capable of avoiding the pathological effects of RNA virus infection, each bat species may have achieved this through distinct pathways, possibly involving changes to both increase pathogen replication control and to mitigate any immunopathology through decreased inflammatory responses and hence increased disease tolerance.

abstract:
  A majority of viruses that have caused recent epidemics with high lethality rates in people, are zoonoses originating from wildlife. Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. Intriguingly, these viruses also all originate from bat reservoirs. Bats have been shown to have a greater mean viral richness than predicted by their phylogenetic distance from humans, their geographic range, or their presence in urban areas, suggesting other traits must explain why bats harbor a greater number of zoonotic viruses than other mammals. Bats are highly unusual among mammals in other ways as well. Not only are they the only mammals capable of powered flight, they have extraordinarily long life spans, with little detectable increases in mortality or senescence until high ages. Their physiology likely impacted their history of pathogen exposure and necessitated adaptations that may have also affected immune signaling pathways. Do our life history traits make us susceptible to generating damaging immune responses to RNA viruses or does the physiology of bats make them particularly tolerant or resistant? Understanding what immune mechanisms enable bats to coexist with RNA viruses may provide critical fundamental insights into how to achieve greater resilience in humans.


id: cord-303941-3lg1bzsi
title: Bats as reservoirs of severe emerging infectious diseases
author: Han, Hui-Ju
date: 2015-07-02
txt: ./txt/cord-303941-3lg1bzsi.txt
cache: ./cache/cord-303941-3lg1bzsi.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S016817021500177X
doi: 10.1016/j.virusres.2015.05.006
summary:
  Although bats are not in close contact with humans, spillover of viruses from bats to intermediate animal hosts, such as horses, pigs, civets, or non-human primates, is thought to be the most likely mode to cause human infection. Currently, bats have been considered to be natural reservoirs of SARS-CoV, MERS-CoV, NiV, HeV, Ebola virus, and Marburg viruses. The viruses discussed above tend to be restricted to certain geographic regions with a particular bat reservoir, such as HeV and NiV associated with flying foxes in Australia and Southeast Asia and Ebola virus associated with Egyptian fruit bats in Africa. Bats have been proposed as the natural reservoirs of viruses causing severe diseases in humans, such as NiV and HeV in Southeast Asia and Australia, Ebola and Marburg viruses in Africa, SARS-CoV in Asia and MERS-CoV in Middle East.

abstract:
  Abstract In recent years severe infectious diseases have been constantly emerging, causing panic in the world. Now we know that many of these terrible diseases are caused by viruses originated from bats (Table 1), such as Ebola virus, Marburg, SARS coronavirus (SARS-CoV), MERS coronavirus (MERS-CoV), Nipah virus (NiV) and Hendra virus (HeV). These viruses have co-evolved with bats due to bats’ special social, biological and immunological features. Although bats are not in close contact with humans, spillover of viruses from bats to intermediate animal hosts, such as horses, pigs, civets, or non-human primates, is thought to be the most likely mode to cause human infection. Humans may also become infected with viruses through aerosol by intruding into bat roosting caves or via direct contact with bats, such as catching bats or been bitten by bats.


id: cord-304481-yqc8r3ll
author: Luis, Angela D.
date: 2015-08-24
txt: ./txt/cord-304481-yqc8r3ll.txt
cache: ./cache/cord-304481-yqc8r3ll.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26299267/
doi: 10.1111/ele.12491
summary:
  Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence. Rodents are a suitable group for comparison because they also host many important zoonotic viruses and share many of the characteristics hypothesised to make bats suitable as viral reservoirs. Host traits that correlated with the highest degree within the bat network (the most connections or viruses shared), in order of importance, were gregariousness and sympatry; diet was marginally important (Fig. 2b, Table S6 and S7). For rodents, sympatry was the most important host trait; species whose distributions overlapped with a greater number of other rodent species had more viruses and higher degree and betweenness (Fig. 2d-f and Table S11-S19).

title:
  Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission

abstract:
  Bats are natural reservoirs of several important emerging viruses. Cross‐species transmission appears to be quite common among bats, which may contribute to their unique reservoir potential. Therefore, understanding the importance of bats as reservoirs requires examining them in a community context rather than concentrating on individual species. Here, we use a network approach to identify ecological and biological correlates of cross‐species virus transmission in bats and rodents, another important host group. We show that given our current knowledge the bat viral sharing network is more connected than the rodent network, suggesting viruses may pass more easily between bat species. We identify host traits associated with important reservoir species: gregarious bats are more likely to share more viruses and bats which migrate regionally are important for spreading viruses through the network. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence.


id: cord-304850-9xetsc2c
title: Virus ecology: a gap between detection and prediction
author: Drosten, Christian
date: 2013-05-22
txt: ./txt/cord-304850-9xetsc2c.txt
cache: ./cache/cord-304850-9xetsc2c.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26038466/
doi: 10.1038/emi.2013.25
abstract: nan
summary:
  7, 8 These and other recent findings remind us of an important issue in viral reservoir ecology: non-persisting viruses are maintained on a social level, requiring large, dense and interconnected host groups for their perpetual transmission. 13 There are prominent examples of bat-borne viruses that can be passed between humans, including Ebola virus, Marburg virus, Nipah virus and the severe acute respiratory syndrome agent. However, there remains a large gap between the many studies describing novel reservoir-borne viruses and our capabilities to use this knowledge to predict or prevent future human disease outbreaks. 13 As we dig deeper into viral reservoir ecology, including its man-made modifications, we may find that changes in host populations affect the transmission and maintenance of viruses with possible consequences for their potential to infect humans (Figure 1 ). Habitat fragmentation Resource abundance Change of social structure Risk Virus replication / transmission Duration of excretion / infectivity Figure 1 Modification of viral maintenance optimum.


id: cord-305024-343l2ha7
title: New Adenovirus in Bats, Germany
author: Sonntag, Michael
date: 2009-12-17
txt: ./txt/cord-305024-343l2ha7.txt
cache: ./cache/cord-305024-343l2ha7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/19961700/
doi: 10.3201/eid1512.090646
summary:
  We performed an extensive search for unknown viruses in 55 German vespertilionid bats based on both generic PCR assays and virus isolation techniques, as part of a broader study investigating histopathologic changes in German bats in association with infectious pathogens. The obtained sequence of a fragment of the DNA polymerase gene (≈550 bp) indicated that the viruses were a novel virus type within the genus Mastadenovirus and was tentatively named bat adenovirus 2 (bat AdV-2) strain P. Although viruses were not detected by various generic PCR assays from homogenized frozen tissue samples, we isolated a novel virus from a hibernating insectivorous bat species. The acquired partial sequence of the bat AdV-2 DNA polymerase with the closest relation to canine adenovirus (only 74% at the nucleic acid level) and the isolation from a new animal host suggests that this virus is a new adenovirus species within the genus Mastadenovirus.

abstract:
  We tested 55 deceased vespertilionid bats of 12 species from southern Germany for virus infections. A new adenovirus was isolated from tissue samples of 2 Pipistrellus pipistrellus bats, which represents the only chiropteran virus isolate found in Europe besides lyssavirus (rabies virus). Evidence was found for adenovirus transmission between bats.


id: cord-305857-2409me0p
title: Seroprevalence Dynamics of European Bat Lyssavirus Type 1 in a Multispecies Bat Colony
author: López-Roig, Marc
date: 2014-09-04
txt: ./txt/cord-305857-2409me0p.txt
cache: ./cache/cord-305857-2409me0p.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v6093386
doi: 10.3390/v6093386
summary:
  In recent years, bats have been implicated in numerous emerging infectious disease events and have been recognized as important reservoir hosts for viruses that can cross the species barrier to infect humans and other domestic and wild mammals [3] . Persistent viral infections occurring among long-lived bats, coupled with their often gregarious roosting behavior, could greatly increase the potential for intra-and inter-species transmission of viruses [7] , especially in summer and winter periods. To study the variation in EBLV-1-antibody prevalence, we conducted two analyses: first, three explanatory variables (sex, species and year) were first screened using a univariate analysis and a chi-square test to check for statistically significant associations with serological status (0: negative; 1: positive). We report the results of the prevalence of specific EBLV-1 neutralizing antibody analysis from the 2004-2012 period in nine bat species roosting in the same refuge.

abstract:
  We report an active surveillance study of the occurrence of specific antibodies to European Bat Lyssavirus Type 1 (EBLV-1) in bat species, scarcely studied hitherto, that share the same refuge. From 2004 to 2012, 406 sera were obtained from nine bat species. Blood samples were subjected to a modified fluorescent antibody virus neutralization test to determine the antibody titer. EBLV-1-neutralizing antibodies were detected in six of the nine species analyzed (Pipistrellus pipistrellus, P. kuhlii, Hypsugo savii, Plecotus austriacus, Eptesicus serotinus and Tadarida teniotis). Among all bats sampled, female seroprevalence (20.21%, 95% CI: 14.78%–26.57%) was not significantly higher than the seroprevalence in males (15.02%, 95% CI: 10.51%–20.54%). The results showed that the inter-annual variation in the number of seropositive bats in T. teniotis and P. austriacus showed a peak in 2007 (>70% of EBLV-1 prevalence). However, significant differences were observed in the temporal patterns of the seroprevalence modeling of T. teniotis and P. austriacus. The behavioral ecology of these species involved could explain the different annual fluctuations in EBLV-1 seroprevalence.


id: cord-308614-gsgntf4c
title: Venipuncture in bats
author: Eshar, David
date: 2010
txt: ./txt/cord-308614-gsgntf4c.txt
cache: ./cache/cord-308614-gsgntf4c.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/laban0610-175
doi: 10.1038/laban0610-175
summary:
  Equipment needed includes a 1-to 3-ml syringe or 0.5-ml insulin syringe; 25-or 27-gauge needles; microtainer collection tubes with heparin and calcium-EDTA; microhematocrit capillary tubes and sealing clay; glass slides; chlorhexidine-based scrub equivalent to 1% of the total body weight at each draw. Venipuncture of the cephalic and the saphenous (interfemoral) veins are two of the best techniques for quick and safe collection of blood in bats. A 25-gauge needle can be used to puncture the vessel in small bats, and the tube can be inserted into the hub of the needle to collect the sample, or if a vein is accidently punctured, blood can be collected into a microhematocrit capillary tube directly from the incision site 2 (Fig. 1) . Venipuncture of the cephalic and saphenous veins without anesthesia usually requires one phlebotomist and one or two individuals to restraint the bat.

abstract:
  Though not as common as small rodents in laboratory settings, bats are being increasingly used in research studies. Knowledge of proper blood sampling techniques is essential for care and management of bats.


id: cord-308932-pp8etmwq
title: Antiviral Immune Responses of Bats: A Review
author: Baker, M. L.
date: 2012-08-01
txt: ./txt/cord-308932-pp8etmwq.txt
cache: ./cache/cord-308932-pp8etmwq.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/23302292/
doi: 10.1111/j.1863-2378.2012.01528.x
summary:
  Efforts to understand the immune systems of bats have been greatly facilitated in recent years by the availability of partial genome sequences from two species of bats, a megabat, Pteropus vampyrus, and a microbat, Myotis lucifugus, allowing the rapid identification of immune genes. Efforts to understand the immune systems of bats have been greatly facilitated in recent years by the availability of partial genome sequences from two species of bats, a megabat, Pteropus vampyrus, and a microbat, Myotis lucifugus, allowing the rapid identification of immune genes. Consistent with the results obtained from bats immunized with /X174 or SRBC antigens, vaccination and experimental viral infections have provided evidence for quantitative and qualitative differences in antibody responses in bats compared with other mammals. It is evident they have similar antibody and T-cell receptor genes, cytokines and chemokines, transcription factors, cluster of differentiation (CD) markers and activation pathways found in the immune responses of other mammalian species.

abstract:
  Despite being the second most species‐rich and abundant group of mammals, bats are also among the least studied, with a particular paucity of information in the area of bat immunology. Although bats have a long history of association with rabies, the emergence and re‐emergence of a number of viruses from bats that impact human and animal health has resulted in a resurgence of interest in bat immunology. Understanding how bats coexist with viruses in the absence of disease is essential if we are to begin to develop therapeutics to target viruses in humans and susceptible livestock and companion animals. Here, we review the current status of knowledge in the field of bat antiviral immunology including both adaptive and innate mechanisms of immune defence and highlight the need for further investigations in this area. Because data in this field are so limited, our discussion is based on both scientific discoveries and theoretical predictions. It is hoped that by provoking original, speculative or even controversial ideas or theories, this review may stimulate further research in this important field. Efforts to understand the immune systems of bats have been greatly facilitated in recent years by the availability of partial genome sequences from two species of bats, a megabat, Pteropus vampyrus, and a microbat, Myotis lucifugus, allowing the rapid identification of immune genes. Although bats appear to share most features of the immune system with other mammals, several studies have reported qualitative and quantitative differences in the immune responses of bats. These observations warrant further investigation to determine whether such differences are associated with the asymptomatic nature of viral infections in bats.


id: cord-309512-d8n9711b
author: Bacus, Michael G.
date: 2020-05-05
txt: ./txt/cord-309512-d8n9711b.txt
cache: ./cache/cord-309512-d8n9711b.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.05.04.076281
doi: 10.1101/2020.05.04.076281
summary:
  Emerging infectious diseases due to coronavirus (CoV) infections have received significant global attention in the past decade and have been linked to bats as the original source. As such, deviant patterns were observed such as for 2D-IV, wherein cross-taxon transmission due to overlap in bat habitats and geographic range among genetically divergent African bat hosts could have played a strong role on their shared CoV lineages. In fact, a few bat taxa especially the subfamily Pteropodinae were shown to host diverse groups of BetaCoVs. Therefore, ecological imbalances that disturb bat distribution may lead to loss of host specificity through cross-taxon transmission and multi-CoV infection. Importance Bat Betacoronaviruses (BetaCoVs) pose a significant threat to global public health and have been implicated in several epidemics such as the recent pandemic by severe acute respiratory syndrome coronavirus 2. Although bat BetaCoVs are host taxon-specific, their evolutionary pathways are different from evolution with its host.

title:
  Global genetic patterns reveal host tropism versus cross-taxon transmission of bat Betacoronaviruses

abstract:
  Emerging infectious diseases due to coronavirus (CoV) infections have received significant global attention in the past decade and have been linked to bats as the original source. The diversity, distribution, and host associations of bat CoVs were investigated to assess their potential for zoonotic transmission. Phylogenetic, network, and principal coordinate analysis confirmed the classification of betacoronaviruses (BetaCoVs) into five groups (2A to 2E) and a potentially novel group, with further division of 2D into five subgroups. The genetic co-clustering of BetaCoVs among closely related bats reflects host taxon-specificity with each bat family as the host for a specific BetaCoV group, potentially a natural barrier against random transmission. The divergent pathway of BetaCoV and host evolution suggests that the viruses were introduced just prior to bat dispersal and speciation. As such, deviant patterns were observed such as for 2D-IV, wherein cross-taxon transmission due to overlap in bat habitats and geographic range among genetically divergent African bat hosts could have played a strong role on their shared CoV lineages. In fact, a few bat taxa especially the subfamily Pteropodinae were shown to host diverse groups of BetaCoVs. Therefore, ecological imbalances that disturb bat distribution may lead to loss of host specificity through cross-taxon transmission and multi-CoV infection. Hence, initiatives that minimize the destruction of wildlife habitats and limit wildlife-livestock-human interfaces are encouraged to help maintain the natural state of bat BetaCoVs in the wild. Importance Bat Betacoronaviruses (BetaCoVs) pose a significant threat to global public health and have been implicated in several epidemics such as the recent pandemic by severe acute respiratory syndrome coronavirus 2. Here, we show that bat BetaCoVs are predominantly host-specific, which could be a natural barrier against infection of other host types. However, a strong overlap in bat habitat and geographic range may facilitate viral transmission to unrelated hosts, and a few bat families have already been shown to host multi-CoV variants. We predict that continued disturbances on the ecological balance may eventually lead to loss of host specificity. When combined with enhanced wildlife-livestock-human interfaces, spillover to humans may be further facilitated. We should therefore start to define the ecological mechanisms surrounding zoonotic events. Global surveillance should be expanded and strengthened to assess the complete picture of bat coronavirus diversity and distribution and their potential to cause spillover infections.


id: cord-310061-nro623aa
title: Detection of novel coronaviruses in bats in Myanmar
author: Valitutto, Marc T.
date: 2020-04-09
txt: ./txt/cord-310061-nro623aa.txt
cache: ./cache/cord-310061-nro623aa.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32271768/
doi: 10.1371/journal.pone.0230802
summary:
  Historically, bats have been linked to highly pathogenic viruses that pose a serious threat to human health, including the coronaviruses responsible for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), the hemorrhagic ebola and Marburg filoviruses, and paramyxoviruses such as Nipah virus [10, 11, [13] [14] [15] [16] [17] [18] . The 2002-2003 SARS epidemic, the emergence of MERS in people in 2012, and the ongoing COVID-19 pandemic have prompted substantial interest in detecting coronaviruses of bat origin due to public health concern and their pandemic potential [10, [13] [14] [15] [16] [17] [18] . In addition to human-associated CoVs, bats are also hosts of coronaviruses that infect production animals, and have been implicated in the emergence and origin of swine acute diarrhea syndrome (SADS), transmissible gastroenteritis virus (TGEV) in pigs, and porcine epidemic diarrhea (PED), which can cause considerable losses [23] [24] [25] [26] .

abstract:
  The recent emergence of bat-borne zoonotic viruses warrants vigilant surveillance in their natural hosts. Of particular concern is the family of coronaviruses, which includes the causative agents of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and most recently, Coronavirus Disease 2019 (COVID-19), an epidemic of acute respiratory illness originating from Wuhan, China in December 2019. Viral detection, discovery, and surveillance activities were undertaken in Myanmar to identify viruses in animals at high risk contact interfaces with people. Free-ranging bats were captured, and rectal and oral swabs and guano samples collected for coronaviral screening using broadly reactive consensus conventional polymerase chain reaction. Sequences from positives were compared to known coronaviruses. Three novel alphacoronaviruses, three novel betacoronaviruses, and one known alphacoronavirus previously identified in other southeast Asian countries were detected for the first time in bats in Myanmar. Ongoing land use change remains a prominent driver of zoonotic disease emergence in Myanmar, bringing humans into ever closer contact with wildlife, and justifying continued surveillance and vigilance at broad scales.


id: cord-310734-6v7oru2l
author: Bolatti, Elisa M.
date: 2020-04-09
txt: ./txt/cord-310734-6v7oru2l.txt
cache: ./cache/cord-310734-6v7oru2l.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v12040422
doi: 10.3390/v12040422
summary:
  By conventional nucleic acid detection techniques and/or bioinformatics approaches, the genomes of two novel viruses were completely covered clustering into the Papillomaviridae (Tadarida brasiliensis papillomavirus type 1, TbraPV1) and Genomoviridae (Tadarida brasiliensis gemykibivirus 1, TbGkyV1) families. Overall, a large number of phage-related sequences were detected (77.3% of viral read pairs and 39.9% of viral contigs), likely representing the most abundant entities infecting bacteria present in the bat digestive system, which exhibited similarity mostly to the families Inoviridae, Siphoviridae, and Myoviridae ( Table 1 ). Several mammalian viral families, supported by the contigs and sequencing reads, have been identified previously in New World [23, 24, 26] and Old World [17, 18, 89] bat species. Table S4 : Read pairs and contigs classified as similar to viruses and not taxonomical assigned to viral families identified in anal and oral swab samples of Tadarida brasiliensis obtained by metagenomics using Illumina technology.

title:
  A Preliminary Study of the Virome of the South American Free-Tailed Bats (Tadarida brasiliensis) and Identification of Two Novel Mammalian Viruses

abstract:
  Bats provide important ecosystem services as pollinators, seed dispersers, and/or insect controllers, but they have also been found harboring different viruses with zoonotic potential. Virome studies in bats distributed in Asia, Africa, Europe, and North America have increased dramatically over the past decade, whereas information on viruses infecting South American species is scarce. We explored the virome of Tadarida brasiliensis, an insectivorous New World bat species inhabiting a maternity colony in Rosario (Argentina), by a metagenomic approach. The analysis of five pooled oral/anal swab samples indicated the presence of 43 different taxonomic viral families infecting a wide range of hosts. By conventional nucleic acid detection techniques and/or bioinformatics approaches, the genomes of two novel viruses were completely covered clustering into the Papillomaviridae (Tadarida brasiliensis papillomavirus type 1, TbraPV1) and Genomoviridae (Tadarida brasiliensis gemykibivirus 1, TbGkyV1) families. TbraPV1 is the first papillomavirus type identified in this host and the prototype of a novel genus. TbGkyV1 is the first genomovirus reported in New World bats and constitutes a new species within the genus Gemykibivirus. Our findings extend the knowledge about oral/anal viromes of a South American bat species and contribute to understand the evolution and genetic diversity of the novel characterized viruses.


id: cord-313472-skcaw9ls
title: Risk factors for bat contact and consumption behaviors in Thailand; a quantitative study
author: Suwannarong, Kanokwan
date: 2020-06-03
txt: ./txt/cord-313472-skcaw9ls.txt
cache: ./cache/cord-313472-skcaw9ls.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32493260/
doi: 10.1186/s12889-020-08968-z
summary:
  The independent variables, including the sociodemographic information, knowledge, attitudes, practices, and perceptions were as follows: -Humans can get diseases from bats (true vs false) -There are no concerns about getting diseases from bats (true vs false) -Bats can transmit diseases to humans (true vs false) -Bats are economically beneficial to the community (agree vs disagree) -One can contract diseases if exposed to bats (true vs false) -One can contract diseases by drinking water from the same places as bats (true vs false) -One can contract diseases by eating fruits left by bats (true vs false) -Bat guano is safe to use (true vs false) -It is safe to eat bats (true vs false) -There are laws related to hunting bats for consumption (true vs false) -Children are allowed to play with bats (true vs false) -Dead bats that are found are brought home for food (true vs false) -One feels safe in areas where bats live (true vs false)

abstract:
  BACKGROUND: Bats serve as an important reservoir for emerging infectious diseases. Bat contact and consumption, which persists in Asia, poses risks for the transmission of bat-borne infections. METHODS: An analytical cross-sectional survey for risk factors associated with bat contact and consumption behaviors was conducted in ten provinces of Thailand from May 2016 to December 2017. A standardized questionnaire administered through face-to-face interviews was used to collect information from 626 villagers who lived in or nearby areas of high bat density. The questionnaire contained 23 independent variables related to sociodemographic, knowledge, attitudes, practices, and perceptions. RESULTS: The respondents (n = 626) were 285 females and 341 males, mean age of respondents was 47.58 years-old and lived in rural setting. Our results showed that 36.42% of respondents (n(1) = 228) in 10 provinces reported bat contact during the past 6 months. Furthermore, 15.34% of respondents (n(2) = 96) in 9 out of 10 provinces reported of having consumed bat meat in the past 6 months. Risk factors for bat contact included sex (male) (OR = 1.56, 95% CI 1.09–2.28), educational attainment (lower than secondary school) (OR = 1.45, 95% CI 1.02–2.18), and the consideration of bats as being economically beneficial to the community (OR = 3.18, 95% CI 2.03–4.97), while agriculture-related occupation (OR = 0.54, 95% CI 0.37–0.79), knowledge that it is safe to eat bats (OR = 0.58, 95% CI 0.37–0.93), practice of allowing children to play with bats (OR = 0.65, 95% CI 0.44–0.96), and attitude of feeling safe in areas where bats live (OR = 0.56, 95% CI 0.38–0.86) were statistically significant protective factors against bat contact. Risk factors for bat consumption included sex (male) (OR = 2.48, 95% CI 1.49–4.11) and educational attainment (lower than secondary school) (OR = 2.21, 95% CI 1.27–3.85), while knowledge of whether bats are safe to eat (OR = 0.04, 95% CI 0.01–0.25), knowledge of whether there are laws pertaining to hunting bats for consumption (OR = 0.35, 95% CI 0.18–0.71), and the practice of allowing children to play with bats (OR = 0.51, 95% CI 0.31–0.81) were statistically significant protective factors against bat consumption. CONCLUSIONS: This study provides a better understanding of the sociodemographic factors, knowledge, attitudes, perceptions and practices that might influence bat contact and bat consumption behaviors. Information on risk factors can be used for the development of appropriate education and communication interventions to promote proper knowledge, attitudes and practices regarding bats and bat-borne zoonotic diseases in Thailand and other areas in the Southeast Asia region with similar environmental and cultural characteristics.


id: cord-315972-5g2hnk1x
title: Detection of Novel SARS-like and Other Coronaviruses in Bats from Kenya
author: Tong, Suxiang
date: 2009-03-17
txt: ./txt/cord-315972-5g2hnk1x.txt
cache: ./cache/cord-315972-5g2hnk1x.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/19239771/
doi: 10.3201/eid1503.081013
summary:
  The sequence diversity suggests that bats are well-established reservoirs for and likely sources of coronaviruses for many species, including humans. Subsequently, a number of other SARS-like CoVs, as well as CoVs from antigenic groups I and II, were identifi ed from bats in Asia, Europe, and North America, and coronavirus antibodies were detected in African bat species (6) (7) (8) (9) (10) (11) . To characterize the overall diversity of CoV sequences, in this study a phylogenetic tree (Figure 2 ) of the 121-bp fragment of RdRp was generated from 39 coronaviruses from bats in Kenya and 47 selected human and animal coronaviruses from the National Center for Biotechnology Information database based on the Bayesian Monte Carlo Markov Chain method (14) . bats (location 17) were closely related to a SARS-like CoV cluster, including 1 sequence shown in Figure 2 (BtKY15) and another (BtKY16) that was 1 of the 3 low-quality sequences excluded from the tree.

abstract:
  Diverse coronaviruses have been identified in bats from several continents but not from Africa. We identified group 1 and 2 coronaviruses in bats in Kenya, including SARS-related coronaviruses. The sequence diversity suggests that bats are well-established reservoirs for and likely sources of coronaviruses for many species, including humans.


id: cord-316343-u1uup5da
author: Luo, Yun
date: 2018-02-01
txt: ./txt/cord-316343-u1uup5da.txt
cache: ./cache/cord-316343-u1uup5da.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s12250-018-0017-2
doi: 10.1007/s12250-018-0017-2
summary:
  Total RNA was extracted from the hearts, livers, spleens, lungs, kidneys, brains, and intestines of six bats infected with bat coronaviruses HKU9 or GCCDC1 using the High Pure Viral RNA Kit. Partial RdRp representing HKU9 or GCCDC1 were cloned into the pGEM-T-easy Vector (Promega, Madison, WI, USA) and used as a positive control for quantitative analysis. By RT-PCR detection targeting partial RdRP, 46 (8.29%) samples were positive for HKU9 and 13 (2.34%) were positive for GCCDC1 or closely related viruses (Table 1) . A phylogenetic tree was conducted based on the alignment of partial RdRp sequences along with previously reported HKU9, GCCDC1, and related stains, as well as representative strains of other betacoronaviruses. In this study, we identified all bat species positive for coronavirus by sequencing the Cytb gene and found that HKU9 and GCCDC1 were from two different genera, Rousettus and Eonycteris, respectively.

title:
  Longitudinal Surveillance of Betacoronaviruses in Fruit Bats in Yunnan Province, China During 2009–2016

abstract:
  Previous studies indicated that fruit bats carry two betacoronaviruses, BatCoV HKU9 and BatCoV GCCDC1. To investigate the epidemiology and genetic diversity of these coronaviruses, we conducted a longitudinal surveillance in fruit bats in Yunnan province, China during 2009–2016. A total of 59 (10.63%) bat samples were positive for the two betacorona-viruses, 46 (8.29%) for HKU9 and 13 (2.34%) for GCCDC1, or closely related viruses. We identified a novel HKU9 strain, tentatively designated as BatCoV HKU9-2202, by sequencing the full-length genome. The BatCoV HKU9-2202 shared 83% nucleotide identity with other BatCoV HKU9 stains based on whole genome sequences. The most divergent region is in the spike protein, which only shares 68% amino acid identity with BatCoV HKU9. Quantitative PCR revealed that the intestine was the primary infection organ of BatCoV HKU9 and GCCDC1, but some HKU9 was also detected in the heart, kidney, and lung tissues of bats. This study highlights the importance of virus surveillance in natural reservoirs and emphasizes the need for preparedness against the potential spill-over of these viruses to local residents living near bat caves. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12250-018-0017-2) contains supplementary material, which is available to authorized users.


id: cord-317244-4su5on6s
author: Maganga, Gael D.
date: 2014-12-31
txt: ./txt/cord-317244-4su5on6s.txt
cache: ./cache/cord-317244-4su5on6s.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.pone.0115588
doi: 10.1371/journal.pone.0115588
summary:
  In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. To further investigate the presence of the virus in bat populations, a strain-specific real-time RT-PCR assay (primers: GB09-478-F, 59-GGCGGCTCTTAAAAGT-GAATG-39; GB09-478-R, 59-GCGGGGTCAAATTGGTCAT-39; probe: GB09-478-P, 59-TCCAGCACAAACATATCCGAGAAGGCTAG-39) was designed within the initial PCR fragment and was used to test total RNA extracted from mixed liver and spleen samples from each of all the other bat species. In order to determine the organ distribution of this virus in infected bats, total RNA was extracted from heart, liver, spleen, kidney, lung, intestine and brain samples from all 14 real-time RT-PCR-positive bats, as described previously, and screened, using the same strain-specific real-time RT-PCR assay shown above.

title:
  Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity

abstract:
  Bats are known to harbor multiple paramyxoviruses. Despite the creation of two new genera, Aquaparamyxovirus and Ferlavirus, to accommodate this increasing diversity, several recently isolated or characterized viruses remain unclassified beyond the subfamily level. In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. Phylogenetically, BelPV is related to J virus and Beilong virus (BeiPV), two other unclassified paramyxoviruses isolated from rodents. In the diseased BelPV-infected C. afra individual, high viral load was detected in the heart, and the lesions were consistent with those reported in wild rodents and mice experimentally infected by J virus. BelPV was not detected in other tested bat species sharing the same roosting sites and living in very close proximity with C. afra in the two caves sampled, suggesting that this virus may be host-specific for C. afra. The mode of transmission of this paramyxovirus in bat populations remains to be discovered.


id: cord-317813-sisfxdso
title: Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano
author: Banskar, Sunil
date: 2016-11-15
txt: ./txt/cord-317813-sisfxdso.txt
cache: ./cache/cord-317813-sisfxdso.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27845426/
doi: 10.1038/srep36948
summary:
  Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Additionally, 16 S rRNA gene sequencing was performed using Ion Torrent PGM to identify the bacterial communities and screened for the presence of putative human pathogens. Sequence analysis of the cytochrome B (cytB) gene amplified from total extracted DNA of the guano pellets revealed that the collected fecal pellets were from a single bat species i.e. Rousettus leschenaultii, a predominant bat species reported from the Robber''s cave 23 . Further, computation of core microbiome from Ion Torrent sequences of fresh guano revealed the presence of five bacterial phyla i.e. Proteobacteria, Tenericutes, Candidate division TM7, Firmicutes and Actinobacteria but in different proportions (Fig. 5, Supplementary Figure S7 ). Additionally, Ion Torrent sequencing of 16 S rRNA gene provided information about the general bacterial communities with specific emphasis on pathogens among the total communities present in bat guano.

abstract:
  Bats are crucial for proper functioning of an ecosystem. They provide various important services to ecosystem and environment. While, bats are well-known carrier of pathogenic viruses, their possible role as a potential carrier of pathogenic bacteria is under-explored. Here, using culture-based approach, employing multiple bacteriological media, over thousand bacteria were cultivated and identified from Rousettus leschenaultii (a frugivorous bat species), the majority of which were from the family Enterobacteriaceae and putative pathogens. Next, pathogenic potential of most frequently cultivated component of microbiome i.e. Escherichia coli was assessed to identify its known pathotypes which revealed the presence of virulent factors in many cultivated E. coli isolates. Applying in-depth bacterial community analysis using high-throughput 16 S rRNA gene sequencing, a high inter-individual variation was observed among the studied guano samples. Interestingly, a higher diversity of bacterial communities was observed in decaying guano representative. The search against human pathogenic bacteria database at 97% identity, a small proportion of sequences were found associated to well-known human pathogens. The present study thus indicates that this bat species may carry potential bacterial pathogens and advice to study the effect of these pathogens on bats itself and the probable mode of transmission to humans and other animals.


id: cord-318080-cmx3q2sc
author: Amoroso, Maria Grazia
date: 2018-06-12
txt: ./txt/cord-318080-cmx3q2sc.txt
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extension: .txt
mime: text/plain
url: https://doi.org/10.1111/zph.12484
doi: 10.1111/zph.12484
summary:
  In this study, we investigated the presence of various human viral pathogens in 14 different species of bats captured in Central and Southern Italy. Upon sequence analysis, we observed a remarkable genetic diversity among the various bat AstV strains detected in Italy. These findings do not confirm the bat species specificity of AstV, proposed by other authors (Fischer et al., 2016 Astrovirus infection is associated with gastro-enteritis in most animal species, and humans AstVs are regarded as a common cause of viral diarrhoea in children (Mendez, Aguirre-Crespo, Zavala, & Arias, 2007; Xiao et al., 2017) . The potential zoonotic risks associated with bats have attracted the attention of researchers, mostly after the discovery of SARS-like and MERS-like CoVs (two coronaviruses highly pathogenic for humans) in European bat species, although the zoonotic risks posed by bat viruses, likely very limited, should be assessed more properly (Kohl & Kurth, 2014) , in large structured studies.

title:
  Detection and phylogenetic characterization of astroviruses in insectivorous bats from Central‐Southern Italy

abstract:
  In recent years, bats have been found to harbour many viruses, raising several questions about their role as reservoirs and potential disseminators of zoonotic viruses. We investigated the presence of six virus families in bats in three regions of Central‐Southern Italy. Astroviruses were identified in seven of 13 bat species. Sequence analysis revealed marked genetic heterogeneity among the astroviruses identified, with nucleotide identity ranging between 60.26% and 87.62%. Astrovirus diversity was not associated with the bat species, the geographic areas or the bat colony, suggesting the circulation of several astrovirus strains in Italian ecosystems. Genetic diversification and interspecies transmission appear common in bat astroviruses and could provide, potentially, the bases for transmission to humans and other mammals. Yet overemphasizing this risk might have detrimental consequences for bat conservation and preservation of the important ecosystem services bats provide.


id: cord-323307-nu9ib62h
title: The genomes of two bat species with long constant frequency echolocation calls
author: Dong, Dong
date: 2016-10-26
txt: ./txt/cord-323307-nu9ib62h.txt
cache: ./cache/cord-323307-nu9ib62h.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/molbev/msw231
doi: 10.1093/molbev/msw231
summary:
  For homology-based gene prediction, the protein sequences of human, mouse, dog, cow, little brown bat and large flying fox were downloaded from Ensembl Release 72 and mapped onto the repeat-masked genome using GenBlastA (She, et al. Moreover, we identified 577, 453 and 182 positively selected genes in the great leaf-nosed bat, the Chinese rufous horseshoe bat and the large flying fox, (Supplementary Tables S10, 11, 12), respectively. Clade model C implemented in PAML was employed (Weadick and Chang 2012) , and the result also persisted that more positively selected genes were detected in the branches leading to echolocating bats (Supplementary Table S20 ). The genome re-sequencing analysis has been performed based generally on the following considerations: 1) to characterize the genetic diversity and patterns of evolution; 2) to understand the genetic bases of adaptation to high altitude in the great leaf-nosed bats.

abstract:
  Bats can perceive the world by using a wide range of sensory systems, and some of the systems have become highly specialized, such as auditory sensory perception. Among bat species, the Old World leaf-nosed bats and horseshoe bats (rhinolophoid bats) possess the most sophisticated echolocation systems. Here, we reported the whole-genome sequencing and de novo assembles of two rhinolophoid bats – the great leaf-nosed bat (Hipposideros armiger) and the Chinese rufous horseshoe bat (Rhinolophus sinicus). Comparative genomic analyses revealed the adaptation of auditory sensory perception in the rhinolophoid bat lineages, probably resulting from the extreme selectivity used in the auditory processing by these bats. Pseudogenization of some vision-related genes in rhinolophoid bats was observed, suggesting that these genes have undergone relaxed natural selection. An extensive contraction of olfactory receptor gene repertoires was observed in the lineage leading to the common ancestor of bats. Further extensive gene contractions can be observed in the branch leading to the rhinolophoid bats. Such concordance suggested that molecular changes at one sensory gene might have direct consequences for genes controlling for other sensory modalities. To characterize the population genetic structure and patterns of evolution, we re-sequenced the genome of 20 great leaf-nosed bats from four different geographical locations of China. The result showed similar sequence diversity values and little differentiation among populations. Moreover, evidence of genetic adaptations to high altitudes in the great leaf-nosed bats was observed. Taken together, our work provided a useful resource for future research on the evolution of bats.


id: cord-324295-9c1zxjng
author: Bonilla-Aldana, D. Katterine
date: 2020-08-20
txt: ./txt/cord-324295-9c1zxjng.txt
cache: ./cache/cord-324295-9c1zxjng.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1201971220306809?v=s5
doi: 10.1016/j.ijid.2020.08.050
summary:
  Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since there is no effective treatment or vaccine for COVID-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of SARS-CoV-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. Fruit bats (genus Pteropus) are the main natural reservoir for Nipah virus (NiV), while pigs serve as intermediate hosts ( Table 3 ). Influenza A viruses (IAV) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (Table 2) .

title:
  Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses

abstract:
  Bats have populated earth for approximately 52 million years, serving as natural reservoirs for a variety of viruses through the course of evolution. Transmission of highly pathogenic viruses from bats has been suspected and linked to a spectrum of emerging infectious diseases in humans and animals worldwide. Examples of such viruses include Marburg, Ebola, Nipah, Hendra, Influenza A, Dengue, Equine Encephalitis viruses, Lyssaviruses, Madariaga and Coronaviruses, involving the now pandemic Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, we provide a comprehensive review on the diversity, reservoirs, and geographical distribution of the main bat viruses and their potential for cross-species transmission.


id: cord-324324-8ybfiz8f
title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses
author: Decaro, Nicola
date: 2020-04-14
txt: ./txt/cord-324324-8ybfiz8f.txt
cache: ./cache/cord-324324-8ybfiz8f.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0378113520302935
doi: 10.1016/j.vetmic.2020.108693
summary:
  In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus.

abstract:
  The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2.


id: cord-327534-f2wvh6la
author: Zhou, Peng
date: 2014-08-06
txt: ./txt/cord-327534-f2wvh6la.txt
cache: ./cache/cord-327534-f2wvh6la.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.pone.0103875
doi: 10.1371/journal.pone.0103875
summary:
  To explore the role of bat IRF7 in the regulation of the IFN response, we performed sequence and functional analysis of IRF7 from the pteropid bat, Pteropus alecto. Regions containing putative IRF3 or IRF7 binding sites were identified from 2221 to 270 bp from the ATG of the bat IFN-b gene by comparison with human IFN promoters and cloned into the pGL4.1 expression vector (Promega). Analysis of the putative bat IRF7 promoter region around 1000 bp upstream of the start site of the ORF resulted in the identification of two IFN stimulated response elements (ISREs) and one nuclear factor kappa B (NF-kB) binding site. Our results demonstrate that even with a significant difference in its MyD88 binding region, bat IRF7 is still capable of inducing IFN-a transcription via MyD88 ( Figure 5 ).

title:
  IRF7 in the Australian Black Flying Fox, Pteropus alecto: Evidence for a Unique Expression Pattern and Functional Conservation

abstract:
  As the only flying mammal, bats harbor a number of emerging and re-emerging viruses, many of which cause severe diseases in humans and other mammals yet result in no clinical symptoms in bats. As the master regulator of the interferon (IFN)-dependent immune response, IFN regulatory factor 7 (IRF7) plays a central role in innate antiviral immunity. To explore the role of bat IRF7 in the regulation of the IFN response, we performed sequence and functional analysis of IRF7 from the pteropid bat, Pteropus alecto. Our results demonstrate that bat IRF7 retains the ability to bind to MyD88 and activate the IFN response despite unique changes in the MyD88 binding domain. We also demonstrate that bat IRF7 has a unique expression pattern across both immune and non-immune related tissues and is inducible by double-strand RNA. The broad tissue distribution of IRF7 may provide bats with an enhanced ability to rapidly activate the IFN response in a wider range of tissues compared to other mammals. The importance of IRF7 in antiviral activity against the bat reovirus, Pulau virus was confirmed by siRNA knockdown of IRF7 in bat cells resulting in enhanced viral replication. Our results highlight the importance of IRF7 in innate antiviral immunity in bats.


id: cord-329050-vzsy6xw1
title: Bats and birds as viral reservoirs: A physiological and ecological perspective
author: Nabi, Ghulam
date: 2020-09-22
txt: ./txt/cord-329050-vzsy6xw1.txt
cache: ./cache/cord-329050-vzsy6xw1.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0048969720359015
doi: 10.1016/j.scitotenv.2020.142372
summary:
  These convergent traits in birds and bats and their ecological interactions with domestic animals and humans increase the potential risk of viral spillover transmission and facilitate the emergence of novel viruses that most likely sources of zoonoses with the potential to cause global pandemics. This paper reviews convergent traits in the physiology, immunology and flight-related ecology of birds and bats with the aim of a better understanding of why these species are such important reservoirs of viral zoonoses, and the potential risk of bat and bird viruses infecting humans. The convergent traits of miniaturized body size, enhanced metabolic rate and antioxidant capacity, prolonged lifespan, a short but efficient digestive tract, and possessing some specific immunological features relative to non-flying mammals are thought to be the result of functional constraints on evolution imposed by the demands of powered flight (Thomas and Suthers, 1972; Norberg, 1990; Caviedes-Vidal et al., 2007; Costantini, 2008; Munshi-South and Wilkinson, 2010; Song et al., 2020; ) .

abstract:
  The birds (class Aves) and bats (order Chiroptera, class Mammalia) are well known natural reservoirs of a diverse range of viruses, including some zoonoses. The only extant volant vertebrates, bats and birds have undergone dramatic adaptive radiations that have allowed them to occupy diverse ecological niches and colonize most of the planet. However, few studies have compared the physiology and ecology of these ecologically, and medically, important taxa. Here, we review convergent traits in the physiology, immunology, flight-related ecology of birds and bats that might enable these taxa to act as viral reservoirs and asymptomatic carriers. Many species of birds and bats are well adapted to urban environments and may host more zoonotic pathogens than species that do not colonize anthropogenic habitats. These convergent traits in birds and bats and their ecological interactions with domestic animals and humans increase the potential risk of viral spillover transmission and facilitate the emergence of novel viruses that most likely sources of zoonoses with the potential to cause global pandemics.


id: cord-329617-gzivtsho
title: De novo transcriptome reconstruction and annotation of the Egyptian rousette bat
author: Lee, Albert K.
date: 2015-12-07
txt: ./txt/cord-329617-gzivtsho.txt
cache: ./cache/cord-329617-gzivtsho.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26643810/
doi: 10.1186/s12864-015-2124-x
summary:
  BACKGROUND: The Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. We performed de novo transcriptome assembly using deep RNA sequencing data from 11 distinct tissues from one male and one female bat. Rousettus aegyptiacus, commonly known as the Egyptian rousette bat, has been identified as a natural reservoir host for MARV through ecological, epidemiological, and experimental studies [10, 12, 13, 18, 19, 24] . aegyptiacus from a de novo assembly of RNA sequencing data from 11 tissues isolated from a male and a female bat. Without a common ground for comparison, it was difficult to perform downstream comparative analyses such as differential gene expression analysis; therefore, we combined contigs from all tissues into one unified, nonredundant reference transcriptome (Fig. 1d) . We further assessed biological validity of our transcriptome assembly through gene Ontology (GO) analysis of tissue-specific expression profiles.

abstract:
  BACKGROUND: The Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. With Ebola virus, Marburg virus is a member of the family Filoviridae that causes severe hemorrhagic fever disease in humans and nonhuman primates, but results in little to no pathological consequences in bats. Understanding host-pathogen interactions within reservoir host species and how it differs from hosts that experience severe disease is an important aspect of evaluating viral pathogenesis and developing novel therapeutics and methods of prevention. RESULTS: Progress in studying bat reservoir host responses to virus infection is hampered by the lack of host-specific reagents required for immunological studies. In order to establish a basis for the design of reagents, we sequenced, assembled, and annotated the R. aegyptiacus transcriptome. We performed de novo transcriptome assembly using deep RNA sequencing data from 11 distinct tissues from one male and one female bat. We observed high similarity between this transcriptome and those available from other bat species. Gene expression analysis demonstrated clustering of expression profiles by tissue, where we also identified enrichment of tissue-specific gene ontology terms. In addition, we identified and experimentally validated the expression of novel coding transcripts that may be specific to this species. CONCLUSION: We comprehensively characterized the R. aegyptiacus transcriptome de novo. This transcriptome will be an important resource for understanding bat immunology, physiology, disease pathogenesis, and virus transmission. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2124-x) contains supplementary material, which is available to authorized users.


id: cord-332088-5c77h0of
title: Emerging horizon for bat borne viral zoonoses
author: Beena, V.
date: 2019-10-26
txt: ./txt/cord-332088-5c77h0of.txt
cache: ./cache/cord-332088-5c77h0of.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31803797/
doi: 10.1007/s13337-019-00548-z
summary:
  In Asia and Pacific regions, bats were demonstrated as natural reservoirs for a large number of this types of emerging as well as re-emerging pathogens such as SARS, Ebola, Marburg, Nipha, Hendra, Tioman, Menangle, Australian bat lyssa virus, Rabies and many encephalitis causing viruses in humans and animals [2] . From bats the pathogen get transmitted to humans via intermediate hosts like horses(hendra) and pigs(nipah) and different species of animals get infected by consumption of partially eaten fruits of bats and the chewed out materials of bats after extracting the juice. The first report of a transmission of a viral disease from bats to humans was a rabies virus (RABV) belonging to the Lyssa virus genus [5] . Identification and complete genome analysis of three novel paramyxoviruses, Tuhoko virus 1, 2 and 3, in fruit bats from China

abstract:
  Bats are the only flying placental mammals that constitute the second largest order of mammals and present all around the world except in Arctic, Antarctica and a few oceanic islands. Sixty percent of emerging infectious diseases originating from animals are zoonotic and more than two-thirds of them originate in wildlife. Bats were evolved as a super-mammal for harboring many of the newly identified deadly diseases without any signs and lesions. Their unique ability to fly, particular diet, roosting behavior, long life span, ability to echolocate and critical susceptibility to pathogens make them suitable host to harbor numerous zoonotic pathogens like virus, bacteria and parasite. Many factors are responsible for the emergence of bat borne zoonoses but the most precipitating factor is human intrusions. Deforestation declined the natural habitat and forced the bats and other wild life to move out of their niche. These stressed bats, having lost foraging and behavioral pattern invade in proximity of human habitation. Either directly or indirectly they transmit the viruses to humans and animals. Development of fast detection modern techniques for viruses from the diseased and environmental samples and the lessons learned in the past helped in preventing the severity during the latest outbreaks.


id: cord-333317-oai67igl
title: Biomarkers of Browning in Cold Exposed Siberian Adults
author: Efremova, Agrafena
date: 2020-07-22
txt: ./txt/cord-333317-oai67igl.txt
cache: ./cache/cord-333317-oai67igl.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/nu12082162
doi: 10.3390/nu12082162
summary:
  Using RT-qPCR, we evaluated the peripheral blood mononuclear cells (PBMC) expression profile of regulators of BAT activity (CIDEA, PRDM16), white adipocytes browning (HOXC9 and SLC27A1), and fatty acid β-oxidation (CPT1A) in 150 Siberian healthy miners living at extremely cold temperatures compared to 29 healthy subjects living in thermoneutral conditions. Studies by Palou and colleagues conducted on female rats demonstrated that the expression of regulators of BAT activity (Cidea, Prdm16), WAT browning (Hoxc9 and Slc27a1), and fatty acid β-oxidation (Cpt1a) in both tissues, correlates with the expression of the same modulators in the peripheral blood mononuclear cells (PBMC) upon cold stimulation [19] . This is the first study investigating the expression of browning, beige, and fatty acids utilization regulators in the PBMC of human subjects chronically exposed to extremely cold temperatures compared to controls living in thermoneutral conditions. Cold-exposed subjects enrolled in our study expressed higher levels of the beiging''s marker HOXC9 and lower amounts of the brown adipocytes'' marker CIDEA compared to controls.

abstract:
  Cold-exposure promotes energy expenditure by inducing brown adipose tissue (BAT) thermogenesis, which over time, is also sustained by browning, the appearance, or increase, of brown-like cells into white fat depots. Identification of circulating markers reflecting BAT activity and browning is crucial to study this phenomenon and its triggers, also holding possible implications for the therapy of obesity and metabolic diseases. Using RT-qPCR, we evaluated the peripheral blood mononuclear cells (PBMC) expression profile of regulators of BAT activity (CIDEA, PRDM16), white adipocytes browning (HOXC9 and SLC27A1), and fatty acid β-oxidation (CPT1A) in 150 Siberian healthy miners living at extremely cold temperatures compared to 29 healthy subjects living in thermoneutral conditions. Anthropometric parameters, glucose, and lipid profiles were also assessed. The cold-exposed group showed significantly lower weight, BMI, hip circumference, and PBMC expression of CIDEA, but higher expression of HOXC9 and higher circulating glucose compared to controls. Within the cold-exposed group, BMI, total cholesterol, and the atherogenic coefficient were lower in individuals exposed to low temperatures for a longer time. In conclusion, human PBMC expresses the brown adipocytes marker CIDEA and the browning marker HOXC9, which, varying according to cold-exposure, possibly reflect changes in BAT activation and white fat browning.


id: cord-333914-c150ki1n
title: Identification and characterization of a novel bat polyomavirus in Japan
author: Koba, Ryota
date: 2020-08-20
txt: ./txt/cord-333914-c150ki1n.txt
cache: ./cache/cord-333914-c150ki1n.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32816186/
doi: 10.1007/s11262-020-01789-7
summary:
  A novel polyomavirus (PyV) was identified in the intestinal contents of Japanese eastern bent-wing bats (Miniopterus fuliginosus) via metagenomic analysis. To determine the complete viral genome of these PyV-like sequences, PCR was performed using LA Taq DNA polymerase (Takara Bio, Otsu, Japan) in accordance with the manufacturer''s instructions. A noncoding regulatory region (NCCR) was located between the start of the early region and that of the late region, in line with previous findings for bat PyVs (Fig. 1a and Supplementary Table 1) [9] [10] [11] [12] . MfPyV VP1 displayed less than 72% nucleotide sequence identity with other bat PyVs (Supplementary Table 2 ). MfPyV TAg sequences contained features known to be conserved in TAgs of other bat PyVs, including the highly conserved DnaJ domain (HPDKGG), a retinoblastoma (Rb)-binding motif (LYCNE), and several functional motifs (Supplementary Fig. 2 ). In conclusion, we detected a novel PyV genome sequence in Japanese bats.

abstract:
  A novel polyomavirus (PyV) was identified in the intestinal contents of Japanese eastern bent-wing bats (Miniopterus fuliginosus) via metagenomic analysis. We subsequently sequenced the full genome of the virus, which has been tentatively named Miniopterus fuliginosus polyomavirus (MfPyV). The nucleotide sequence identity of the genome with those of other bat PyVs was less than 80%. Phylogenetic analysis revealed that MfPyV belonged to the same cluster as PyVs detected in Miniopterus schreibersii. This study has identified the presence of a novel PyV in Japanese bats and provided genetic information about the virus. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11262-020-01789-7) contains supplementary material, which is available to authorized users.


id: cord-334027-xhfmio7k
title: Can Bats Serve as Reservoirs for Arboviruses?
author: Fagre, Anna C.
date: 2019-03-03
txt: ./txt/cord-334027-xhfmio7k.txt
cache: ./cache/cord-334027-xhfmio7k.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v11030215
doi: 10.3390/v11030215
summary:
  No demonstrable pathologic effects noted during infection of three bat species [big brown bats (Eptesicus fuscus), little brown bats (Myotis lucifigus) and Mexican free-tailed bats (Tadarida brasiliensie mexicana) with various strains of JBEV or St. Louis encephalitis virus (SLEV) [69] . While experimental data demonstrated that some bat species can sustain JBEV infections and support mosquito-borne transmission of this virus, the epidemiological significance of these observations in the field remains unclear. To truly elucidate the role of bats as reservoirs for arboviruses, field surveillance studies documenting natural infection and transmission dynamics among vector and vertebrate species must be supplemented with experimental infections to characterize viremia profiles and infectiousness to vectors, virus-induced pathology, and immune kinetics following infection. The isolation of Marburg virus from Egyptian rousette bats in Uganda in addition to experimental infections demonstrating viremia and shedding in the absence of overt pathology support the role of this bat species as the reservoir for Marburg virus [6, 7, 208] .

abstract:
  Bats are known to harbor and transmit many emerging and re-emerging viruses, many of which are extremely pathogenic in humans but do not cause overt pathology in their bat reservoir hosts: henipaviruses (Nipah and Hendra), filoviruses (Ebola and Marburg), and coronaviruses (SARS-CoV and MERS-CoV). Direct transmission cycles are often implicated in these outbreaks, with virus shed in bat feces, urine, and saliva. An additional mode of virus transmission between bats and humans requiring further exploration is the spread of disease via arthropod vectors. Despite the shared ecological niches that bats fill with many hematophagous arthropods (e.g., mosquitoes, ticks, biting midges, etc.) known to play a role in the transmission of medically important arboviruses, knowledge surrounding the potential for bats to act as reservoirs for arboviruses is limited. To this end, a comprehensive literature review was undertaken examining the current understanding and potential for bats to act as reservoirs for viruses transmitted by blood-feeding arthropods. Serosurveillance and viral isolation from either free-ranging or captive bats are described in relation to four arboviral groups (Bunyavirales, Flaviviridae, Reoviridae, Togaviridae). Further, ecological associations between bats and hematophagous viral vectors are characterized (e.g., bat bloodmeals in mosquitoes, ingestion of mosquitoes by bats, etc). Lastly, knowledge gaps related to hematophagous ectoparasites (bat bugs and bed bugs (Cimicidae) and bat flies (Nycteribiidae and Streblidae)), in addition to future directions for characterization of bat-vector-virus relationships are described.


id: cord-334628-axon4jdc
title: Genetic Characteristics of Coronaviruses from Korean Bats in 2016
author: Lee, Saemi
date: 2017-07-19
txt: ./txt/cord-334628-axon4jdc.txt
cache: ./cache/cord-334628-axon4jdc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28725945/
doi: 10.1007/s00248-017-1033-8
summary:
  In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1–99.7%) with Bat-CoV-JTMC15 reported in China. Given the import of MERS into South Korea [14] and the presence of SARS in the relatively close geographic location of China [9] (Fig. 3) , together with the fact that bats are a reservoir for coronaviruses, the prevalence of coronavirus infection in Korean bat species should provide valuable information. Oral swabs and other samples (n = 60) were obtained from three species of bats, Rhinolophus ferrumequinum, Miniopterus schreibersii, and Myotis macrodactylus, but coronaviruses were only detected in samples from R. Thirteen sequences from oral swabs were clustered with Bat-CoV B15-21, which was detected in fecal bat samples collected from an abandoned mine in Gangwon province.

abstract:
  Bats have increasingly been recognized as the natural reservoir of severe acute respiratory syndrome (SARS), coronavirus, and other coronaviruses found in mammals. However, little research has been conducted on bat coronaviruses in South Korea. In this study, bat samples (332 oral swabs, 245 fecal samples, 38 urine samples, and 57 bat carcasses) were collected at 33 natural bat habitat sites in South Korea. RT-PCR and sequencing were performed for specific coronavirus genes to identify the bat coronaviruses in different bat samples. Coronaviruses were detected in 2.7% (18/672) of the samples: 13 oral swabs from one species of the family Rhinolophidae, and four fecal samples and one carcass (intestine) from three species of the family Vespertiliodae. To determine the genetic relationships of the 18 sequences obtained in this study and previously known coronaviruses, the nucleotide sequences of a 392-nt region of the RNA-dependent RNA polymerase (RdRp) gene were analyzed phylogenetically. Thirteen sequences belonging to SARS-like betacoronaviruses showed the highest nucleotide identity (97.1–99.7%) with Bat-CoV-JTMC15 reported in China. The other five sequences were most similar to MERS-like betacoronaviruses. Four nucleotide sequences displayed the highest identity (94.1–95.1%) with Bat-CoV-HKU5 from Hong Kong. The one sequence from a carcass showed the highest nucleotide identity (99%) with Bat-CoV-SC2013 from China. These results suggest that careful surveillance of coronaviruses from bats should be continued, because animal and human infections may result from the genetic variants present in bat coronavirus reservoirs.


id: cord-338055-2d6n4cve
title: A unique view of SARS-CoV-2 through the lens of ORF8 protein
author: Hassan, Sk. Sarif
date: 2020-08-26
txt: ./txt/cord-338055-2d6n4cve.txt
cache: ./cache/cord-338055-2d6n4cve.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.08.25.267328
doi: 10.1101/2020.08.25.267328
summary:
  In this present study, we identified the distinct mutations present across unique variants of the SARS-CoV-2 ORF8 and classified them according to their predicted effect on the host, i.e disease or neutral and the consequences on protein structural stability. The ORF8 sequences of SARS-CoV-2, Bat-CoV RaTG13 and Pangolin-CoV have almost the same positive and negative charged amino acids, therefore we can say that probably they have similar kind of electrostatic and hydrophobic interactions, 135 which also contribute to the functionality of the proteins. • QKV07730.1: The T11A mutation occurred as the second mutation in this sequence, which was predicted to be of disease-increasing type and the polarity was changed from hydrophilic to hydrophobic, hence the structure and 305 function of the protein are expected to differ.

abstract:
  Immune evasion is one of the unique characteristics of COVID-19 attributed to the ORF8 protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This protein is involved in modulating the host adaptive immunity through downregulating MHC (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the interferon mediated antiviral response of the host. To understand the immune perspective of the host with respect to the ORF8 protein, a comprehensive study of the ORF8 protein as well as mutations possessed by it, is performed. Chemical and structural properties of ORF8 proteins from different hosts, that is human, bat and pangolin, suggests that the ORF8 of SARS-CoV-2 and Bat RaTG13-CoV are very much closer related than that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 (SARS-CoV-2) are grouped into four classes based on their predicted effects. Based on geolocations and timescale of collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were endorsed upon sequence similarity and amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of rapid evolving SARS-CoV-2 through the ORF8.


id: cord-338400-30vl2hks
author: Epstein, Jonathan H.
date: 2010-07-01
txt: ./txt/cord-338400-30vl2hks.txt
cache: ./cache/cord-338400-30vl2hks.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.ppat.1000972
doi: 10.1371/journal.ppat.1000972
summary:
  Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades. GBV-A viruses have been described in New World primates and are not known to infect humans [17] [18] [19] , while GBV-C (also known as Hepatitis G virus (HGV)) have frequently been isolated from humans in many regions of the World, including India and Bangladesh [19] [20] [21] [22] [23] , and from wild chimpanzees (Pan troglodytes) in Africa [24, 25] . Our findings provide new insight into the range of known hosts for GB-like viruses and demonstrate the power of unbiased sequencing to characterize the diversity of potentially zoonotic pathogens carried by bats and other reservoirs. Molecular analyses of sera from Pteropus giganteus bats from Faridpur, Bangladesh led to the identification of a 9,633 nt sequence consistent in genomic organization with known GBV and other species within the family Flaviviridae [16] .

title:
  Identification of GBV-D, a Novel GB-like Flavivirus from Old World Frugivorous Bats (Pteropus giganteus) in Bangladesh

abstract:
  Bats are reservoirs for a wide range of zoonotic agents including lyssa-, henipah-, SARS-like corona-, Marburg-, Ebola-, and astroviruses. In an effort to survey for the presence of other infectious agents, known and unknown, we screened sera from 16 Pteropus giganteus bats from Faridpur, Bangladesh, using high-throughput pyrosequencing. Sequence analyses indicated the presence of a previously undescribed virus that has approximately 50% identity at the amino acid level to GB virus A and C (GBV-A and -C). Viral nucleic acid was present in 5 of 98 sera (5%) from a single colony of free-ranging bats. Infection was not associated with evidence of hepatitis or hepatic dysfunction. Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades.


id: cord-338586-rkrkofri
title: Bat and virus
author: Shi, Zhengli
date: 2010-02-01
txt: ./txt/cord-338586-rkrkofri.txt
cache: ./cache/cord-338586-rkrkofri.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s13238-010-0029-7
doi: 10.1007/s13238-010-0029-7
summary:
  Bats are recently identified as natural reservoir of SARS-CoV that caused outbreaks of human respiratory disease during 2002-2003 in China and resulted in 8422 cases with 916 deaths in 29 countries and regions (Chan-Yeung and Xu, 2003) . Filoviruses Marburg virus and Ebola virus, belonging to the family Filoviridae, are two emerging viruses that cause human hemorrhagic fever disease (HF) (Sanchez et al., 2007) . Other Bat CoVs During the search for the origin of SARS-CoV, numerous novel CoVs were detected in large numbers of bat species in China, South and North America, Germany and Africa (Poon et al., 2005; Chu et al., 2006; Ren et al., 2006; Tang et al., 2006; Dominguez et al., 2007; Lau et al., 2007; Muller et al., 2007; Woo et al., 2007; Carrington et al., 2008; Gloza-Rausch et al., 2008; Misra et al., 2009; Pfefferle et al., 2009) .

abstract:
  Bat, the only flying mammal and count more than 20% of the extant mammals on earth, were recently identified as a natural reservoir of emerging and reemerging infectious pathogens. Astonishing amount (more than 70) and genetic diversity of viruses isolated from the bat have been identified in different populations throughout the world. Many studies focus on bat viruses that caused severe domestic and human diseases. However, many viruses were found in apparently healthy bats, suggesting that bats may have a specific immune system or antiviral activity against virus infections. Therefore, basic researches for bat immunology and virus-host interactions are important for understanding bat-derived infectious diseases.


id: cord-342124-jdv17u86
author: Nieto‐Rabiela, Fabiola
date: 2019-06-20
txt: ./txt/cord-342124-jdv17u86.txt
cache: ./cache/cord-342124-jdv17u86.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/zph.12618
doi: 10.1111/zph.12618
summary:
  title: Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis To address this gap in knowledge, we compared the associative capacity of the host–virus networks in rodents and bats with the identification of those viruses with zoonotic potential. (2015) analyse viral networks between rodents and bats at global scale identifying several ecology factors to explain virus-host associations. The parameter "betweenness" can be used to Impacts • The analysis of virus and host networks (rodents and bats) allows us to measure the potential risk of zoonotic diseases. • Measuring network connectivity can be a useful tool for identifying hosts and viruses of potential importance in the transmission dynamic of zoonotic diseases. Therefore, in this study we aimed to compare and recognize the differences in the associative capacity of the host-virus networks in rodents and bats worldwide, as well as to identify the viruses that may shift across species, including humans, suggesting zoonotic potential.

title:
  Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis

abstract:
  Bats and rodents are recognized to host a great diversity of viruses and several important viral zoonoses, but how this viral diversity is structured and how viruses are connected, shared and distributed among host networks is not well understood. To address this gap in knowledge, we compared the associative capacity of the host–virus networks in rodents and bats with the identification of those viruses with zoonotic potential. A virus database, detected by molecular methods, was constructed in the two taxonomic groups. We compiled 5,484 records: 825 in rodents and 4,659 in bats. We identified a total of 173 and 166 viruses, of which 53 and 40 are zoonotic viruses, in rodents and bats, respectively. Based on a network theory, a non‐directed bipartite host–virus network was built for each group. Subsequently, the networks were collapsed to represent the connections among hosts and viruses. We identified both discrete and connected communities. We observed a greater degree of connectivity in bat viruses and more discrete communities in rodents. The Coronaviridae recorded in bats have the highest values of degree, betweenness and closeness centralities. In rodents, higher degree positions were distributed homogeneously between viruses and hosts. At least in our database, a higher proportion of rodent viruses were zoonotic. Rodents should thus not be underestimated as important reservoirs of zoonotic disease. We found that viruses were more frequently shared among bats than in rodents. Network theory can reveal some macroecological patterns and identify risks that were previously unrecognized. For example, we found that parvovirus in megabats and Gbagroube virus in rodents may represent a zoonotic risk due to the proximity to humans and other zoonotic viruses. We propose that epidemiological surveillance programmes should consider the connectivity of network actors as a measure of the risks of dispersion and transmission.


id: cord-343206-9tqivs5f
title: Extreme temperature event and mass mortality of insectivorous bats
author: Pruvot, Mathieu
date: 2019-04-29
txt: ./txt/cord-343206-9tqivs5f.txt
cache: ./cache/cord-343206-9tqivs5f.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32214949/
doi: 10.1007/s10344-019-1280-8
summary:
  A mass mortality event involving Chaerephon plicatus and Taphozous theobaldi bats occurred during a heat wave in April 2016 in Cambodia. Systematic documentation of bat die-offs related to extreme weather events is necessary to improve understanding of the effect of changing weather patterns on bat populations and the ecosystem services they provide. Although the effects of climate change on wildlife populations is increasingly documented (FAO 2012) , there is still much to learn about the responses of particular species to extreme temperature events, and the potential consequences for their populations and the ecosystem services they support. Systematically documenting mass mortality events is important to understand how bat populations could be affected by a changing environment and climate (Welbergen et al. As such, this report contributes to documenting how changes in land-use and weather patterns influence bat population resilience and health.

abstract:
  A mass mortality event involving Chaerephon plicatus and Taphozous theobaldi bats occurred during a heat wave in April 2016 in Cambodia. This was investigated to clarify the causes of the die-off and assess the risk to public health. Field evidences, clinical signs, and gross pathology findings were consistent with a heat stress hypothesis. However, the detection of a novel bat paramyxovirus raises questions about its role as a contributing factor or a coincidental finding. Systematic documentation of bat die-offs related to extreme weather events is necessary to improve understanding of the effect of changing weather patterns on bat populations and the ecosystem services they provide.


id: cord-345695-5vi9wibk
title: A statistical approach to white-nose syndrome surveillance monitoring using acoustic data
author: Hicks, Lorin L.
date: 2020-10-22
txt: ./txt/cord-345695-5vi9wibk.txt
cache: ./cache/cord-345695-5vi9wibk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33091068/
doi: 10.1371/journal.pone.0241052
summary:
  From these data, we developed site-specific prediction models for bat activity to account for seasonal and annual temperature variation prior to known occurrence of WNS. We propose this model-based method for future monitoring efforts that could be used to trigger targeted sampling of individual bats or hibernacula for WNS, in areas where traditional disease surveillance approaches are logistically difficult to implement or because of human-wildlife transmission concerns from COVID-19. We predicted that bat populations in the western U.S. would have low levels of activity during winter months, high levels of activity during the summer, and that acoustic monitoring could be used as an effective approach for disease surveillance in remote areas of the Intermountain West. The model was fit to data from all 41 sites to estimate among-site and among-year variation in activity, but we use the results to generate prediction intervals for four forest sites to depict how a landowner might implement this approach for WNS surveillance monitoring.

abstract:
  Traditional pathogen surveillance methods for white-nose syndrome (WNS), the most serious threat to hibernating North American bats, focus on fungal presence where large congregations of hibernating bats occur. However, in the western USA, WNS-susceptible bat species rarely assemble in large numbers and known winter roosts are uncommon features. WNS increases arousal frequency and activity of infected bats during hibernation. Our objective was to explore the effectiveness of acoustic monitoring as a surveillance tool for WNS. We propose a non-invasive approach to model pre-WNS baseline activity rates for comparison with future acoustic data after WNS is suspected to occur. We investigated relationships among bat activity, ambient temperatures, and season prior to presence of WNS across forested sites of Montana, USA where WNS was not known to occur. We used acoustic monitors to collect bat activity and ambient temperature data year-round on 41 sites, 2011–2019. We detected a diverse bat community across managed (n = 4) and unmanaged (n = 37) forest sites and recorded over 5.37 million passes from bats, including 13 identified species. Bats were active year-round, but positive associations between average of the nightly temperatures by month and bat activity were strongest in spring and fall. From these data, we developed site-specific prediction models for bat activity to account for seasonal and annual temperature variation prior to known occurrence of WNS. These prediction models can be used to monitor changes in bat activity that may signal potential presence of WNS, such as greater than expected activity in winter, or less than expected activity during summer. We propose this model-based method for future monitoring efforts that could be used to trigger targeted sampling of individual bats or hibernacula for WNS, in areas where traditional disease surveillance approaches are logistically difficult to implement or because of human-wildlife transmission concerns from COVID-19.


id: cord-347532-n51qv9pp
title: Group C Betacoronavirus in Bat Guano Fertilizer, Thailand
author: Wacharapluesadee, Supaporn
date: 2013-08-17
txt: ./txt/cord-347532-n51qv9pp.txt
cache: ./cache/cord-347532-n51qv9pp.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3201/eid1908.130119
doi: 10.3201/eid1908.130119
abstract: nan
summary:
  To the Editor: Bats play a critical role in the transmission and origin of zoonotic diseases, primarily viral zoonoses associated with high casefatality rates, including those caused by Nipah virus (NiV) and severe acute respiratory syndrome (SARS)-like coronavirus (CoV) infections (1) . To assess pathogens in bat guano, we examined bat guano from a cave in the Khao Chong Phran Non-hunting Area (KCP-NHA) in Ratchaburi Province, Thailand, where bat guano was sold as agricultural fertilizer, for the presence of NiV, CoV, and H. The detection of CoVs in bat guano from the KCP-NHA cave in Ratchaburi was consistent with the previous finding of alphacoronavirus from Hipposideros armiger bats from the same province in 2007, but those researchers tested fresh bat feces (9) . Duplex nested RT-PCR for detection of Nipah virus RNA from urine specimens of bats


id: cord-350286-n7ylgqfu
author: Giri, Rajanish
date: 2020-04-03
txt: ./txt/cord-350286-n7ylgqfu.txt
cache: ./cache/cord-350286-n7ylgqfu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.03.13.990598
doi: 10.1101/2020.03.13.990598
summary:
  The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) .

title:
  When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses

abstract:
  Recently emerged coronavirus designated as SARS-CoV-2 (also known as 2019 novel coronavirus (2019-nCoV) or Wuhan coronavirus) is a causative agent of coronavirus disease 2019 (COVID-19), which is rapidly spreading throughout the world now. More than 9,00,000 cases of SARS-CoV-2 infection and more than 47,000 COVID-19-associated mortalities have been reported worldwide till the writing of this article, and these numbers are increasing every passing hour. World Health Organization (WHO) has declared the SARS-CoV-2 spread as a global public health emergency and admitted that the COVID-19 is a pandemic now. The multiple sequence alignment data correlated with the already published reports on the SARS-CoV-2 evolution and indicated that this virus is closely related to the bat Severe Acute Respiratory Syndrome-like coronavirus (bat SARS-like CoV) and the well-studied Human SARS coronavirus (SARS CoV). The disordered regions in viral proteins are associated with the viral infectivity and pathogenicity. Therefore, in this study, we have exploited a set of complementary computational approaches to examine the dark proteomes of SARS-CoV-2, bat SARS-like, and human SARS CoVs by analysing the prevalence of intrinsic disorder in their proteins. According to our findings, SARS-CoV-2 proteome contains very significant levels of structural order. In fact, except for Nucleocapsid, Nsp8, and ORF6, the vast majority of SARS-CoV-2 proteins are mostly ordered proteins containing less intrinsically disordered protein regions (IDPRs). However, IDPRs found in SARS-CoV-2 proteins are functionally important. For example, cleavage sites in its replicase 1ab polyprotein are found to be highly disordered, and almost all SARS-CoV-2 proteins were shown to contain molecular recognition features (MoRFs), which are intrinsic disorder-based protein-protein interaction sites that are commonly utilized by proteins for interaction with specific partners. The results of our extensive investigation of the dark side of the SARS-CoV-2 proteome will have important implications for the structural and non-structural biology of SARS or SARS-like coronaviruses. Significance The infection caused by a novel coronavirus (SARS-CoV-2) that causes severe respiratory disease with pneumonia-like symptoms in humans is responsible for the current COVID-19 pandemic. No in-depth information on structures and functions of SARS-CoV-2 proteins is currently available in the public domain, and no effective anti-viral drugs and/or vaccines are designed for the treatment of this infection. Our study provides the first comparative analysis of the order- and disorder-based features of the SARS-CoV-2 proteome relative to human SARS and bat CoV that may be useful for structure-based drug discovery.


id: cord-352361-jh31omg2
author: Nobach, Daniel
date: 2020-01-30
txt: ./txt/cord-352361-jh31omg2.txt
cache: ./cache/cord-352361-jh31omg2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32000801/
doi: 10.1186/s12985-020-1289-3
summary:
  Although several rodents and other small mammals are known as important reservoirs for many viruses, bats (order: Chiroptera) represent the vast majority of identified natural reservoirs of several virus families/species to date [1, 14] . In conclusion, due to the continuous detection of new viruses in bats, the unclear situation regarding additional potential BoDV-1-reservoirs and molecular evidence for co-evolution of bats and bornaviruses, this study was conducted to investigate the potential presence of the most common orthobornaviruses in bats from endemic and non-endemic areas in Germany. Although the bicolored white-toothed shrew has been identified as indigenous reservoir of BoDV-1, other potential reservoirs or animal carriers are still unknown so that further investigations of small mammals including bat species are urgently needed. Distribution of Borna disease virus antigen and RNA in tissues of naturally infected bicolored white-toothed shrews, Crocidura leucodon, supporting their role as reservoir host species

title:
  No evidence for European bats serving as reservoir for Borna disease virus 1 or other known mammalian orthobornaviruses

abstract:
  BACKGROUND: The majority of emerging infectious diseases are zoonotic in nature and originate from wildlife reservoirs. Borna disease, caused by Borna disease virus 1 (BoDV-1), is an infectious disease affecting mammals, but recently it has also been shown to cause fatal encephalitis in humans. The endemic character of Borna disease points towards a nature-bound reservoir, with only one shrew species identified as reservoir host to date. Bats have been identified as reservoirs of a variety of zoonotic infectious agents. Endogenous borna-like elements in the genome of certain bat species additionally point towards co-evolution of bats with bornaviruses and therefore raise the question whether bats could serve as a potential reservoir of orthobornaviruses. METHODS: Frozen brain samples (n = 257) of bats of seven different genera from Germany were investigated by orthobornaviral RT-PCR. Additionally, tissue slides of formalin-fixed paraffin-embedded material of a subset of these bats (n = 140) were investigated for orthobornaviral phosphoprotein by immunohistochemistry. RESULTS: The brain samples were tested by RT-PCR without any evidence of orthobornavirus specific amplicons. Immunohistochemistry revealed a faint immunoreaction in 3/140 bats but with an untypical staining pattern for viral antigen. CONCLUSIONS: RT-PCR-screening showed no evidence for orthobornaviral RNA in the investigated bats. However, immunohistochemistry results should be investigated further to elucidate whether the reaction might be associated with expressed endogenous bornaviral elements or other so far unknown bornaviruses.


id: cord-352563-yb446bap
author: Li, Ya
date: 2019-05-20
txt: ./txt/cord-352563-yb446bap.txt
cache: ./cache/cord-352563-yb446bap.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31110296/
doi: 10.1038/s41434-019-0081-8
summary:
  Bat AAVs could only slightly infect mouse liver but could transduce mouse muscle to some extent after systemic administration with a higher muscle/liver ratio than that of primate AAVs. Bat AAV 10HB showed moderate muscle transduction, similar to that of AAV2, during direct intramuscular injection and, compared with other AAV serotypes, was also relatively efficient in resisting human antibody neutralization after intramuscular injection. In this study, a number of bat AAV capsid genes will be cloned and characterized with a focus on their tissue tropism and immunological properties, which will establish a foundation for their further application in gene therapy, especially in the presence of human AAV antibodies. Considering both its moderate transduction of mouse muscle and efficient evasion of human antibody neutralization, the bat AAV 10HB vector exhibited the potential to be used for muscular gene therapy in humans.

title:
  Bat adeno-associated viruses as gene therapy vectors with the potential to evade human neutralizing antibodies

abstract:
  The prevalence of adeno-associated virus (AAV) has been investigated in bat populations, but little is known about the biological properties of this virus. In this study, four full-length bat AAV capsid genes were isolated in China, with their amino acid sequences sharing 61% identity with those of AAV2 on average. These capsid genes could package AAV particles in combination with AAV2 rep and ITRs, albeit at a lower efficiency. Bat AAVs could only slightly infect mouse liver but could transduce mouse muscle to some extent after systemic administration with a higher muscle/liver ratio than that of primate AAVs. Bat AAV 10HB showed moderate muscle transduction, similar to that of AAV2, during direct intramuscular injection and, compared with other AAV serotypes, was also relatively efficient in resisting human antibody neutralization after intramuscular injection. Evolutionary analysis revealed a number of codons in bat AAV capsid genes subject to positive selection, with sites corresponding to V259 and N691 in 10HB capsids being localized on the surface of the AAV2 capsid. Mutagenesis studies indicated that the positive selection in bat AAV capsids is driven by their tropism evolution in host species. Taken together, the results of this study indicate that bat AAV 10HB vector has the possible applications for muscular gene therapy, especially in the presence of human AAV neutralizing antibodies.


id: cord-354738-4rxradwz
title: European Bats as Carriers of Viruses with Zoonotic Potential
author: Kohl, Claudia
date: 2014-08-13
txt: ./txt/cord-354738-4rxradwz.txt
cache: ./cache/cord-354738-4rxradwz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25123684/
doi: 10.3390/v6083110
summary:
  In this review, selected viruses detected and isolated in Europe are discussed from our point of view in regard to their human-pathogenic potential. Various publications reviewed bats globally as carriers and potential reservoir hosts of human-pathogenic and zoonotic viruses [3] [4] [5] [6] [7] [8] [9] [10] , while hardly anything is known about human-pathogenicity of European bat viruses apart from lyssaviruses. Similar to the case of the LLOV filovirus, virus isolates and prevalence studies in both humans and bats could improve knowledge and clarify their zoonotic potential. Sero-prevalence studies should be conducted on the orthoreoviruses isolated from European bats, especially as a closely related virus was detected in a diseased child in Slovenia [83] . Other bat viruses detected by using molecular techniques should be isolated (e.g., MERS-like CoV or Bat Bunyavirus) to allow for characterization and follow-up sero-prevalence studies.

abstract:
  Bats are being increasingly recognized as reservoir hosts of highly pathogenic and zoonotic emerging viruses (Marburg virus, Nipah virus, Hendra virus, Rabies virus, and coronaviruses). While numerous studies have focused on the mentioned highly human-pathogenic bat viruses in tropical regions, little is known on similar human-pathogenic viruses that may be present in European bats. Although novel viruses are being detected, their zoonotic potential remains unclear unless further studies are conducted. At present, it is assumed that the risk posed by bats to the general public is rather low. In this review, selected viruses detected and isolated in Europe are discussed from our point of view in regard to their human-pathogenic potential. All European bat species and their roosts are legally protected and some European species are even endangered. Nevertheless, the increasing public fear of bats and their viruses is an obstacle to their protection. Educating the public regarding bat lyssaviruses might result in reduced threats to both the public and the bats.


id: cord-355075-ieb35upi
title: The immune gene repertoire of an important viral reservoir, the Australian black flying fox
author: Papenfuss, Anthony T
date: 2012-06-20
txt: ./txt/cord-355075-ieb35upi.txt
cache: ./cache/cord-355075-ieb35upi.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1471-2164-13-261
doi: 10.1186/1471-2164-13-261
summary:
  alecto transcriptome provides information on a variety of immune genes not previously identified in any bat species and represents an important starting point for examining the antiviral activity of these molecules. To enrich for sequences corresponding to cytokines and innate immune genes, the second dataset was derived from pooled total RNA obtained from mitogen-stimulated spleen, white blood cells and lymph node and unstimulated thymus and bone marrow obtained from one pregnant female and one adult male flying fox. A full length transcript, encoding a 667 amino acid protein was identified in our bat transcriptome datasets and found to be orthologous to Mx1 based on comparison with known mammalian Mx1 and Mx2 family members (Figure 4a and data not shown). Genes involved in the adaptive immune system, including MHC class I and II genes and T and B cell receptors and co-receptors were highly represented in both the thymus and pooled datasets providing evidence that bats have all of the components necessary to mount an adaptive immune response.

abstract:
  BACKGROUND: Bats are the natural reservoir host for a range of emerging and re-emerging viruses, including SARS-like coronaviruses, Ebola viruses, henipaviruses and Rabies viruses. However, the mechanisms responsible for the control of viral replication in bats are not understood and there is little information available on any aspect of antiviral immunity in bats. Massively parallel sequencing of the bat transcriptome provides the opportunity for rapid gene discovery. Although the genomes of one megabat and one microbat have now been sequenced to low coverage, no transcriptomic datasets have been reported from any bat species. In this study, we describe the immune transcriptome of the Australian flying fox, Pteropus alecto, providing an important resource for identification of genes involved in a range of activities including antiviral immunity. RESULTS: Towards understanding the adaptations that have allowed bats to coexist with viruses, we have de novo assembled transcriptome sequence from immune tissues and stimulated cells from P. alecto. We identified about 18,600 genes involved in a broad range of activities with the most highly expressed genes involved in cell growth and maintenance, enzyme activity, cellular components and metabolism and energy pathways. 3.5% of the bat transcribed genes corresponded to immune genes and a total of about 500 immune genes were identified, providing an overview of both innate and adaptive immunity. A small proportion of transcripts found no match with annotated sequences in any of the public databases and may represent bat-specific transcripts. CONCLUSIONS: This study represents the first reported bat transcriptome dataset and provides a survey of expressed bat genes that complement existing bat genomic data. In addition, these data provide insight into genes relevant to the antiviral responses of bats, and form a basis for examining the roles of these molecules in immune response to viral infection.


id: cord-355737-o0y4rn0z
author: Ng, Melinda
date: 2015-12-23
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url: https://doi.org/10.7554/elife.11785
doi: 10.7554/elife.11785
summary:
  To assess whether the EBOV infection defect in the African straw-colored fruit bat cells occurs at the viral entry step, we exposed an expanded panel of kidney fibroblast cell lines from four African pteropodids to VSV pseudotypes bearing GP spikes (VSV-GP) from seven filoviruses, including two non-African viruses, Reston virus (RESTV) and Lloviu virus (LLOV) ( Figure 1D ). Like the infection defect in African straw-colored fruit bat cells, this receptor binding defect was selective for EBOV GP, since GPs derived from MARV and the European filovirus, LLOV (Ng et al., 2014) , bound equivalently to all four pteropodid domain Cs ( Figure 4A ). . We conclude that a species-specific defect in virus-receptor interaction, caused by a single amino acid residue change in EhNPC1 relative to other, permissive African pteropodid NPC1 orthologs, reduces EBOV infection in African straw-colored fruit bat cells.

title:
  Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats

abstract:
  Biological factors that influence the host range and spillover of Ebola virus (EBOV) and other filoviruses remain enigmatic. While filoviruses infect diverse mammalian cell lines, we report that cells from African straw-colored fruit bats (Eidolon helvum) are refractory to EBOV infection. This could be explained by a single amino acid change in the filovirus receptor, NPC1, which greatly reduces the affinity of EBOV-NPC1 interaction. We found signatures of positive selection in bat NPC1 concentrated at the virus-receptor interface, with the strongest signal at the same residue that controls EBOV infection in Eidolon helvum cells. Our work identifies NPC1 as a genetic determinant of filovirus susceptibility in bats, and suggests that some NPC1 variations reflect host adaptations to reduce filovirus replication and virulence. A single viral mutation afforded escape from receptor control, revealing a pathway for compensatory viral evolution and a potential avenue for expansion of filovirus host range in nature. DOI: http://dx.doi.org/10.7554/eLife.11785.001


