Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 99 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 5172 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 51 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 94 bat 25 virus 19 SARS 14 RNA 6 specie 6 Fig 5 gene 5 figure 5 MERS 5 Bat 4 human 4 dna 4 Pteropus 4 PCR 4 IFN 3 infection 3 host 3 european 3 Thailand 3 Supplementary 3 Ebola 3 China 2 strain 2 sequence 2 population 2 guano 2 egyptian 2 coronavirus 2 cell 2 WAT 2 Table 2 Nipah 2 Italy 2 India 2 Africa 1 zoonotic 1 vp7 1 viral 1 vascular 1 tissue 1 sympathetic 1 supplementary 1 spp 1 social 1 site 1 sample 1 rodent 1 rate 1 rabies 1 protein Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 10490 bat 5005 virus 2176 specie 1672 study 1644 sequence 1623 % 1443 gene 1398 host 1369 infection 1334 cell 1215 protein 1093 disease 985 analysis 916 human 904 sample 886 coronavirus 792 animal 756 reservoir 752 genome 691 transmission 685 population 633 group 630 site 615 region 601 datum 596 tissue 591 fruit 583 response 572 coronaviruse 561 number 522 family 491 antibody 487 mammal 470 cov 469 result 468 diversity 457 evidence 450 pathogen 450 level 446 mouse 445 receptor 440 model 439 strain 430 role 422 syndrome 411 expression 410 figure 409 risk 403 genus 399 rodent Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 2008 al 1659 et 1544 . 1190 SARS 688 RNA 679 CoV 492 CoVs 466 Bat 418 Fig 408 PCR 308 Table 306 P. 298 Nipah 288 Pteropus 285 China 283 CoV-2 271 MERS 258 IFN 234 Africa 228 Ebola 219 IRF7 216 Myotis 216 Human 209 C 202 R. 177 Marburg 174 Hendra 173 M. 171 East 167 Europe 166 USA 164 RT 162 PVAT 157 Rousettus 155 T. 154 alecto 151 S 150 Chiroptera 145 E. 140 South 133 MARV 130 World 128 AAV 126 Germany 125 indirubin 124 Middle 124 Asia 122 Australia 120 ORF8 118 aegyptiacus Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 1433 we 790 it 443 they 190 i 142 them 43 us 26 he 16 themselves 13 itself 9 she 9 one 8 you 2 clustalx 1 ours 1 mg 1 http://gpminer.mbc.nctu.edu 1 hp6a 1 hku4-covs 1 him 1 grch37 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 15238 be 3094 have 1885 use 855 identify 851 include 837 show 740 detect 738 find 619 associate 558 relate 546 suggest 517 emerge 478 know 462 report 452 do 452 base 448 infect 443 provide 401 cause 394 indicate 391 isolate 366 follow 355 increase 354 compare 350 contain 334 perform 328 collect 325 describe 311 obtain 309 reveal 283 occur 280 observe 272 demonstrate 265 determine 251 represent 250 result 241 support 235 bind 227 test 225 predict 220 induce 214 remain 212 fly 212 bear 207 consider 206 belong 198 share 198 make 192 involve 188 sample Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 1341 human 1227 not 1213 other 1118 viral 1025 also 920 high 812 - 698 different 643 more 577 only 565 however 522 zoonotic 515 novel 492 such 491 respiratory 479 important 477 most 457 like 455 large 453 immune 439 new 426 further 419 positive 417 genetic 414 low 384 specific 383 well 365 several 365 natural 358 severe 357 acute 351 first 342 long 341 many 339 phylogenetic 327 same 320 similar 306 infectious 303 non 302 molecular 302 likely 301 potential 293 highly 287 mammalian 286 previously 275 recent 264 respectively 264 multiple 260 small 260 significant Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 160 most 76 high 72 least 60 large 50 Most 41 good 26 close 17 low 11 great 9 small 8 long 8 early 5 old 5 late 4 short 3 strong 3 preS1 3 near 3 molossid 2 young 2 broad 2 big 1 ≈200 1 wide 1 steady 1 slight 1 simple 1 poor 1 hot 1 few 1 dry 1 dense 1 bad 1 N)-NS7a 1 Least 1 ClustalW Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 317 most 64 least 9 well 2 oldest 2 long 1 highest 1 early 1 clustalw Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 11 doi.org 5 talk.ictvonline.org 4 www.ncbi.nlm.nih.gov 4 www.mdpi.com 4 orcid.org 3 tree.bio.ed.ac.uk 3 github.com 2 www.who.int 2 www.mgc.ac.cn 2 www.mgc.ac 2 www.mgc 2 pave.niaid.nih.gov 2 dx.doi.org 2 creativecommons.org 1 wwwnc 1 www2c.cdc.gov 1 www.uniprot.org 1 www.technelysium.com.au 1 www.repeatmasker.org 1 www.repeatmasker 1 www.nrbsc.org 1 www.ncbi.nlm 1 www.mammalsociety.org 1 www.iucnredlist.org 1 www.geoboundaries.org 1 www.genome.jp 1 www.genomatix.de 1 www.cdc.gov 1 www.cbs.dtu.dk 1 www.animalpv.org 1 www 1 vietnam.opendevelopmentmekong.net 1 uswest.ensembl.org 1 thomsonreuters.com 1 sourceforge.net 1 sg.idtdna.com 1 rsb.info.nih.gov 1 repeatmasker.org 1 proteomics.ysu.edu 1 osp.od.nih.gov 1 ictvonline.org 1 host13.bioinfo3.ifomieocampus.it 1 hmmer.org 1 gpminer.mbc.nctu.edu 1 genomics.senescence.info 1 genome.ucsc.edu 1 emboss.bioinformatics.nl 1 ecogenomics.github 1 ec.europa 1 eartheng Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 4 http://doi.org/10 3 http://tree.bio.ed.ac.uk/software/figtree/ 2 http://www.mgc.ac.cn/DRodVir/ 2 http://www.mgc.ac 2 http://www.mgc 2 http://pave.niaid.nih.gov/ 2 http://doi.org/10.1016/j.vetmic.2020.108693 2 http://creativecommons.org/licenses/by/4.0/ 1 http://wwwnc 1 http://www2c.cdc.gov/podcasts/player.asp?f=8632573 1 http://www.who.int/csr/ 1 http://www.who.int/ 1 http://www.uniprot.org/help/uniref 1 http://www.technelysium.com.au/ChromasPro.html 1 http://www.repeatmasker.org/genomic 1 http://www.repeatmasker 1 http://www.nrbsc.org/gfx/genedoc/ 1 http://www.ncbi.nlm.nih.gov/gorf/Orfig.cgi 1 http://www.ncbi.nlm.nih.gov/genome 1 http://www.ncbi.nlm.nih.gov/genbank/ 1 http://www.ncbi.nlm.nih.gov/ 1 http://www.ncbi.nlm 1 http://www.mdpi.com/2414-6366/4/3/99/s1 1 http://www.mdpi.com/2072-6643/12/8/2162/s1 1 http://www.mdpi.com/1999-4915/12/4/422/s1 1 http://www.mdpi.com/1999-4915/11/4/356/ 1 http://www.mammalsociety.org/committees/animal-care-anduse 1 http://www.iucnredlist.org/technical-documents/spatial-data 1 http://www.geoboundaries.org 1 http://www.genome.jp/dbget-bin/www_bget?hsa: 1 http://www.genomatix.de/cgi-bin//matinspector_prof 1 http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/ 1 http://www.cbs.dtu.dk/services/ 1 http://www.animalpv.org/ 1 http://www 1 http://vietnam.opendevelopmentmekong.net 1 http://uswest.ensembl.org/index.html 1 http://thomsonreuters.com/products_services/science 1 http://talk.ictvonline.org/taxonomy/ 1 http://talk.ictvonline.org/ictvreports/ictv_online_report/introduction/ 1 http://talk.ictvonline.org/ictv-reports/ 1 http://talk.ictvonline.org/ 1 http://talk.ictvonline.org 1 http://sourceforge.net/projects/glean-gene/ 1 http://sg.idtdna.com/site 1 http://rsb.info.nih.gov/ij/ 1 http://repeatmasker.org 1 http://proteomics.ysu.edu/ 1 http://osp.od.nih.gov/sites/default/files/NIH_Guidelines 1 http://orcid.org/0000-0002-9840-2360 Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 zlshi@wh.iov.cn Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 33 bats are natural 11 bats are not 10 bats are also 10 samples were then 9 genomes provides insight 9 virus was first 8 bats are capable 6 bats are reservoirs 6 bats do not 6 samples reveals many 6 samples were positive 5 bats are able 5 bats are likely 5 bats are more 5 bats are susceptible 5 bats have also 5 genes were also 5 genome reveals unexpected 5 samples reveals more 5 study did not 5 viruses were present 4 analysis reveals insights 4 bats are common 4 bats are important 4 bats are less 4 bats are often 4 bats are special 4 bats are well 4 bats did not 4 bats have not 4 bats is important 4 bats is likely 4 bats is not 4 cells were then 4 sequences were also 4 species are more 4 species were not 4 studies have also 4 virus is not 4 virus was also 4 viruses have not 4 viruses is not 3 bats are extremely 3 bats are highly 3 bats are increasingly 3 bats are particularly 3 bats are potential 3 bats does not 3 bats have long 3 bats have more Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 bats is not well 1 animals is not yet 1 bat has no well 1 bats are no longer 1 bats are not consistent 1 bats are not likely 1 bats are not only 1 bats are not well 1 bats are not widespread 1 bats does not necessarily 1 bats does not significantly 1 bats has not yet 1 bats have no laryngeal 1 bats have not only 1 bats is not as 1 bats is not unique 1 bats revealed no evidence 1 bats was not really 1 bats were not continually 1 bats were not individually 1 cells were no longer 1 genomes contain no more 1 host has not yet 1 humans are not available 1 humans has not yet 1 humans is not simple 1 infection is not specific 1 infection was not completely 1 population are not advisable 1 population are not clear 1 reservoir has not yet 1 rna provided no evidence 1 sequence is not obvious 1 sequences do not either 1 site was not independent 1 species are not simple 1 species was not clearly 1 species were not independent 1 species were not susceptible 1 studies are not directly 1 studies are not feasible 1 studies found no evidence 1 studies reveal no imminent 1 virus had not previously 1 virus has not yet 1 virus is not globally 1 virus is not sufficient 1 viruses do not currently 1 viruses had not yet 1 viruses is not surprising A rudimentary bibliography -------------------------- id = cord-256452-77xij0fc author = Allen, Louise C. title = Roosting ecology and variation in adaptive and innate immune system function in the Brazilian free-tailed bat (Tadarida brasiliensis) date = 2008-11-11 keywords = PHA; bat 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. doi = 10.1007/s00360-008-0315-3 id = cord-318080-cmx3q2sc author = Amoroso, Maria Grazia title = Detection and phylogenetic characterization of astroviruses in insectivorous bats from Central‐Southern Italy date = 2018-06-12 keywords = Italy; bat 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. doi = 10.1111/zph.12484 id = cord-262815-fg76s168 author = Anthony, S. J. title = Coronaviruses in bats from Mexico date = 2013-05-01 keywords = Mexico; bat 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) . doi = 10.1099/vir.0.049759-0 id = cord-309512-d8n9711b author = Bacus, Michael G. title = Global genetic patterns reveal host tropism versus cross-taxon transmission of bat Betacoronaviruses date = 2020-05-05 keywords = bat 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. doi = 10.1101/2020.05.04.076281 id = cord-262434-q4tk96tq author = Baker, Kate S. title = Poxviruses in Bats … so What? date = 2014-04-03 keywords = bat; host; poxvirus 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. doi = 10.3390/v6041564 id = cord-308932-pp8etmwq author = Baker, M. L. title = Antiviral Immune Responses of Bats: A Review date = 2012-08-01 keywords = IFN; Pteropus; bat 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. doi = 10.1111/j.1863-2378.2012.01528.x id = cord-017785-zwnkrs23 author = Baker, Michelle L. title = Mammalia: Chiroptera: Immunology of Bats date = 2018-03-10 keywords = IFN; Pteropus; bat; cell 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. doi = 10.1007/978-3-319-76768-0_23 id = cord-295433-olmein3q author = Banerjee, Arinjay title = Bats and Coronaviruses date = 2019-01-09 keywords = MERS; SARS; bat; virus 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] . doi = 10.3390/v11010041 id = cord-317813-sisfxdso author = Banskar, Sunil title = Microbiome analysis reveals the abundance of bacterial pathogens in Rousettus leschenaultii guano date = 2016-11-15 keywords = Ion; Torrent; bacterial; bat; guano 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. doi = 10.1038/srep36948 id = cord-332088-5c77h0of author = Beena, V. title = Emerging horizon for bat borne viral zoonoses date = 2019-10-26 keywords = China; India; bat; virus 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 doi = 10.1007/s13337-019-00548-z id = cord-310734-6v7oru2l author = Bolatti, Elisa M. title = 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 keywords = Genomoviridae; Rep; bat; dna; sequence 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. doi = 10.3390/v12040422 id = cord-324295-9c1zxjng author = Bonilla-Aldana, D. Katterine title = Bats in Ecosystems and their Wide Spectrum of Viral Infectious Threats: SARS-CoV-2 and other emerging viruses date = 2020-08-20 keywords = SARS; bat; figure; human; virus 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) . doi = 10.1016/j.ijid.2020.08.050 id = cord-287131-svtdfeop author = Campos, Angélica Cristine Almeida title = Bat Influenza A(HL18NL11) Virus in Fruit Bats, Brazil date = 2019-02-17 keywords = HL18NL11; bat 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. doi = 10.3201/eid2502.181246 id = cord-103460-5thh6syt author = Carlson, Colin J. title = Climate change will drive novel cross-species viral transmission date = 2020-07-14 keywords = bat; viral 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 . doi = 10.1101/2020.01.24.918755 id = cord-274620-6ebl319q author = Ceballos, Nidia Aréchiga title = Novel Lyssavirus in Bat, Spain date = 2013-05-17 keywords = IKOV; bat 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. doi = 10.3201/eid1905.121071 id = cord-257321-l1swyr6g author = Chen, Lihong title = DRodVir: A resource for exploring the virome diversity in rodents date = 2017-05-20 keywords = bat; rodent; virus 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. doi = 10.1016/j.jgg.2017.04.004 id = cord-006502-6ajms947 author = Cheng, Chak Kwong title = Perivascular Adipose Tissue: the Sixth Man of the Cardiovascular System date = 2018-08-31 keywords = IL-6; PVAT; WAT; adipose; bat; sympathetic; tissue; vascular 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 doi = 10.1007/s10557-018-6820-z id = cord-003757-uwbpbai7 author = Chionh, Yok Teng title = High basal heat-shock protein expression in bats confers resistance to cellular heat/oxidative stress date = 2019-06-22 keywords = Fig; HSP70; bat; cell 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. doi = 10.1007/s12192-019-01013-y id = cord-286708-igu984oc author = Chua, Kaw Bing title = Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections date = 2008-11-25 keywords = Kampar; NBV; bat; virus 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. doi = 10.1371/journal.pone.0003803 id = cord-272009-yxjhfg7m author = Cui, Jie title = Evolutionary Relationships between Bat Coronaviruses and Their Hosts date = 2007-10-17 keywords = SARS; bat 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. doi = 10.3201/eid1310.070448 id = cord-324324-8ybfiz8f author = Decaro, Nicola title = Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date = 2020-04-14 keywords = China; East; IBV; MERS; RNA; SARS; bat; coronavirus 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. doi = 10.1016/j.vetmic.2020.108693 id = cord-323307-nu9ib62h author = Dong, Dong title = The genomes of two bat species with long constant frequency echolocation calls date = 2016-10-26 keywords = bat; chinese; gene; supplementary 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. doi = 10.1093/molbev/msw231 id = cord-304850-9xetsc2c author = Drosten, Christian title = Virus ecology: a gap between detection and prediction date = 2013-05-22 keywords = bat; virus 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. doi = 10.1038/emi.2013.25 id = cord-333317-oai67igl author = Efremova, Agrafena title = Biomarkers of Browning in Cold Exposed Siberian Adults date = 2020-07-22 keywords = BMI; PBMC; bat; cold 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. doi = 10.3390/nu12082162 id = cord-021805-2j07zw6q author = Epstein, Jonathan H. title = Emerging Diseases in Bats date = 2018-09-28 keywords = Ebola; SARS; bat; virus 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. doi = 10.1016/b978-0-323-55228-8.00040-0 id = cord-338400-30vl2hks author = Epstein, Jonathan H. title = Identification of GBV-D, a Novel GB-like Flavivirus from Old World Frugivorous Bats (Pteropus giganteus) in Bangladesh date = 2010-07-01 keywords = GBV; bat; virus 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] . doi = 10.1371/journal.ppat.1000972 id = cord-308614-gsgntf4c author = Eshar, David title = Venipuncture in bats date = 2010 keywords = bat; blood 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. doi = 10.1038/laban0610-175 id = cord-334027-xhfmio7k author = Fagre, Anna C. title = Can Bats Serve as Reservoirs for Arboviruses? date = 2019-03-03 keywords = Artibeus; Uganda; bat; egyptian; infection; japanese; virus 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] . doi = 10.3390/v11030215 id = cord-350286-n7ylgqfu author = Giri, Rajanish 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 date = 2020-04-03 keywords = Bat; Human; RNA; SARS; Supplementary; Table; figure; protein 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) . doi = 10.1101/2020.03.13.990598 id = cord-261547-8tfbhmzo author = Góes, Luiz Gustavo Bentim title = Genetic diversity of bats coronaviruses in the Atlantic Forest hotspot biome, Brazil date = 2016-07-26 keywords = bat 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. doi = 10.1016/j.meegid.2016.07.034 id = cord-265357-3f0xph0y author = Halczok, Tanja K. 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 date = 2017-01-05 keywords = NRW; bat; genetic; population 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. doi = 10.1186/s12862-016-0856-0 id = cord-303941-3lg1bzsi author = Han, Hui-Ju title = Bats as reservoirs of severe emerging infectious diseases date = 2015-07-02 keywords = Ebola; MERS; SARS; bat 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. doi = 10.1016/j.virusres.2015.05.006 id = cord-338055-2d6n4cve author = Hassan, Sk. Sarif title = A unique view of SARS-CoV-2 through the lens of ORF8 protein date = 2020-08-26 keywords = Bat; ORF8; Pangolin; SARS 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. doi = 10.1101/2020.08.25.267328 id = cord-345695-5vi9wibk author = Hicks, Lorin L. title = A statistical approach to white-nose syndrome surveillance monitoring using acoustic data date = 2020-10-22 keywords = Montana; WNS; activity; bat 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. doi = 10.1371/journal.pone.0241052 id = cord-005012-bgo0uwob author = Hiller, Thomas title = Host Biology and Anthropogenic Factors Affect Hepadnavirus Infection in a Neotropical Bat date = 2018-12-18 keywords = Drexler; TBHBV; bat 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. doi = 10.1007/s10393-018-1387-5 id = cord-293946-4bquxdqa author = Huong, Nguyen Quynh title = Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014 date = 2020-08-10 keywords = Nam; Nguyen; SARS; Viet; bat 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. doi = 10.1371/journal.pone.0237129 id = cord-256370-cz88t29n author = Jansen van Vuren, Petrus title = Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa date = 2016-02-29 keywords = MAHLV; RNA; Vero; bat; virus 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) . doi = 10.3390/v8030065 id = cord-294698-mtfrbn87 author = Kim, H. K. title = Detection of Severe Acute Respiratory Syndrome‐Like, Middle East Respiratory Syndrome‐Like Bat Coronaviruses and Group H Rotavirus in Faeces of Korean Bats date = 2016-05-23 keywords = B15; Bat; SARS 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. doi = 10.1111/tbed.12515 id = cord-333914-c150ki1n author = Koba, Ryota title = Identification and characterization of a novel bat polyomavirus in Japan date = 2020-08-20 keywords = bat; dna 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. doi = 10.1007/s11262-020-01789-7 id = cord-287748-co9j3uig author = Kobayashi, Tomoya title = Detection of bat hepatitis E virus RNA in microbats in Japan date = 2018-05-29 keywords = RNA; bat 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. doi = 10.1007/s11262-018-1577-9 id = cord-354738-4rxradwz author = Kohl, Claudia title = European Bats as Carriers of Viruses with Zoonotic Potential date = 2014-08-13 keywords = Europe; MERS; bat; european 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. doi = 10.3390/v6083110 id = cord-003232-nquw7qga author = Kuchipudi, Suresh V. title = Novel Flu Viruses in Bats and Cattle: “Pushing the Envelope” of Influenza Infection date = 2018-08-06 keywords = bat; influenza; virus 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. doi = 10.3390/vetsci5030071 id = cord-329617-gzivtsho author = Lee, Albert K. title = De novo transcriptome reconstruction and annotation of the Egyptian rousette bat date = 2015-12-07 keywords = Fig; bat; gene 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. doi = 10.1186/s12864-015-2124-x id = cord-334628-axon4jdc author = Lee, Saemi title = Genetic Characteristics of Coronaviruses from Korean Bats in 2016 date = 2017-07-19 keywords = Bat; MERS; SARS 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. doi = 10.1007/s00248-017-1033-8 id = cord-003775-1axsebya author = Lelli, Davide title = Hypsugopoxvirus: A Novel Poxvirus Isolated from Hypsugo savii in Italy date = 2019-06-19 keywords = HYPV; Italy; bat 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. doi = 10.3390/v11060568 id = cord-352563-yb446bap author = Li, Ya title = Bat adeno-associated viruses as gene therapy vectors with the potential to evade human neutralizing antibodies date = 2019-05-20 keywords = AAV; AAV2; bat; capsid 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. doi = 10.1038/s41434-019-0081-8 id = cord-295554-0pzjyrdf author = Lima, Francisco Esmaile de Sales title = Detection of Alphacoronavirus in velvety free-tailed bats (Molossus molossus) and Brazilian free-tailed bats (Tadarida brasiliensis) from urban area of Southern Brazil date = 2013-03-16 keywords = Brazil; bat 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) . doi = 10.1007/s11262-013-0899-x id = cord-295727-s63lffi8 author = Lima, Luciana title = Trypanosoma livingstonei: a new species from African bats supports the bat seeding hypothesis for the Trypanosoma cruzi clade date = 2013-08-03 keywords = Megatrypanum; Trypanosoma; bat; figure 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. doi = 10.1186/1756-3305-6-221 id = cord-102977-yci9kq6x author = Liu, Haiming title = GHSR-1a is not Required for Ghrelin’s Anti-inflammatory and Fat-sparing Effects in Cancer Cachexia date = 2019-12-06 keywords = WAT; bat 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. doi = 10.1101/866376 id = cord-304481-yqc8r3ll author = Luis, Angela D. title = Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission date = 2015-08-24 keywords = Fig; bat; specie; virus 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). doi = 10.1111/ele.12491 id = cord-316343-u1uup5da author = Luo, Yun title = Longitudinal Surveillance of Betacoronaviruses in Fruit Bats in Yunnan Province, China During 2009–2016 date = 2018-02-01 keywords = HKU9; PCR; bat; gccdc1 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. doi = 10.1007/s12250-018-0017-2 id = cord-305857-2409me0p author = López-Roig, Marc title = Seroprevalence Dynamics of European Bat Lyssavirus Type 1 in a Multispecies Bat Colony date = 2014-09-04 keywords = EBLV-1; bat; specie 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. doi = 10.3390/v6093386 id = cord-010307-sxh5mq1q author = MILNE, D. J. title = Structure and environmental relationships of insectivorous bat assemblages in tropical Australian savannas date = 2005-11-23 keywords = Australia; bat; end; site; specie 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. doi = 10.1111/j.1442-9993.2005.01535.x id = cord-284367-cy61pjcb author = MULEYA, Walter title = Molecular Epidemiology of Paramyxoviruses in Frugivorous Eidolon helvum Bats in Zambia date = 2013-12-31 keywords = PCR; bat 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) . doi = 10.1292/jvms.13-0518 id = cord-317244-4su5on6s author = Maganga, Gael D. title = Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date = 2014-12-31 keywords = PCR; RNA; bat; virus 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. doi = 10.1371/journal.pone.0115588 id = cord-003482-f1uvohf0 author = Malmlov, Ashley title = Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date = 2019-02-04 keywords = RNA; ZIKV; Zika; bat; virus 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. doi = 10.1371/journal.pntd.0007071 id = cord-297790-tpjxt0w5 author = Mandl, Judith N. title = Going to Bat(s) for Studies of Disease Tolerance date = 2018-09-20 keywords = IFN; RNA; bat; dna; infection; virus 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. doi = 10.3389/fimmu.2018.02112 id = cord-270143-muxrxvyo author = Markotter, Wanda title = Paramyxo- and Coronaviruses in Rwandan Bats date = 2019-07-02 keywords = Africa; RNA; USA; bat 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] . doi = 10.3390/tropicalmed4030099 id = cord-271687-sxl8g85p author = Mathews, Fiona title = Chapter 8 Zoonoses in Wildlife: Integrating Ecology into Management date = 2009-03-14 keywords = United; bat; european; population 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. doi = 10.1016/s0065-308x(08)00608-8 id = cord-281956-obwtd33y author = Mayer, Fabiana Quoos title = Pathogenic Leptospira spp. in bats: Molecular investigation in Southern Brazil date = 2017-05-12 keywords = Leptospira; bat; spp 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. doi = 10.1016/j.cimid.2017.05.003 id = cord-017407-nc9cyu2u author = Mehlhorn, Heinz title = Introduction: The World of Bats date = 2013-09-03 keywords = bat 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. doi = 10.1007/978-3-642-39333-4_1 id = cord-277039-yo5ojr0s author = Mendenhall, Ian H. title = Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan date = 2019-04-17 keywords = Kazakhstan; SARS; bat 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. doi = 10.3390/v11040356 id = cord-021152-6znmkvy9 author = Montecino-Latorre, Diego title = Reproduction of East-African bats may guide risk mitigation for coronavirus spillover date = 2020-02-07 keywords = SARS; bat; coronavirus; detection; specie 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] ), doi = 10.1186/s42522-019-0008-8 id = cord-289555-1z4vbldd author = Mühldorfer, Kristin title = Diseases and Causes of Death in European Bats: Dynamics in Disease Susceptibility and Infection Rates date = 2011-12-28 keywords = Germany; bat; european; specie 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) . doi = 10.1371/journal.pone.0029773 id = cord-329050-vzsy6xw1 author = Nabi, Ghulam title = Bats and birds as viral reservoirs: A physiological and ecological perspective date = 2020-09-22 keywords = bat; bird; virus 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; ) . doi = 10.1016/j.scitotenv.2020.142372 id = cord-355737-o0y4rn0z author = Ng, Melinda title = Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats date = 2015-12-23 keywords = EBOV; Ebola; NPC1; african; bat; figure 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. doi = 10.7554/elife.11785 id = cord-342124-jdv17u86 author = Nieto‐Rabiela, Fabiola title = Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis date = 2019-06-20 keywords = bat; virus; zoonotic 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. doi = 10.1111/zph.12618 id = cord-284015-vvtv492b author = Nikaido, Masato title = Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera date = 2020-09-23 keywords = Fig; Supplementary; bat; egyptian; gene; megabat 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. doi = 10.1093/dnares/dsaa021 id = cord-352361-jh31omg2 author = Nobach, Daniel title = No evidence for European bats serving as reservoir for Borna disease virus 1 or other known mammalian orthobornaviruses date = 2020-01-30 keywords = Borna; RNA; bat 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 doi = 10.1186/s12985-020-1289-3 id = cord-003166-k3jxvzfi author = Noh, Ji Yeong title = Isolation and characterization of novel bat paramyxovirus B16-40 potentially belonging to the proposed genus Shaanvirus date = 2018-08-22 keywords = B16; KBPV; bat; virus 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. doi = 10.1038/s41598-018-30319-7 id = cord-277306-r8jki3x4 author = Osborne, Christina title = Alphacoronaviruses in New World Bats: Prevalence, Persistence, Phylogeny, and Potential for Interaction with Humans date = 2011-05-12 keywords = Colorado; RNA; World; bat 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) . doi = 10.1371/journal.pone.0019156 id = cord-355075-ieb35upi author = Papenfuss, Anthony T title = The immune gene repertoire of an important viral reservoir, the Australian black flying fox date = 2012-06-20 keywords = MHC; RNA; bat; gene; sequence 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. doi = 10.1186/1471-2164-13-261 id = cord-291965-9r9ll83m author = Pfefferle, Susanne title = Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana date = 2009-09-17 keywords = MRCA; RNA; SARS; bat 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. doi = 10.3201/eid1509.090224 id = cord-343206-9tqivs5f author = Pruvot, Mathieu title = Extreme temperature event and mass mortality of insectivorous bats date = 2019-04-29 keywords = bat 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. doi = 10.1007/s10344-019-1280-8 id = cord-001455-n7quwr4s author = Rapin, Noreen title = Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans date = 2014-11-12 keywords = PCR; bat; infection 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. doi = 10.1371/journal.pone.0112285 id = cord-254713-ghcwfcx2 author = Razanajatovo, Norosoa H title = Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar date = 2015-03-12 keywords = Madagascar; RNA; bat; specie 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. doi = 10.1186/s12985-015-0271-y id = cord-272250-asuxx1ln author = Robertson, Kis title = Rabies-Related Knowledge and Practices Among Persons At Risk of Bat Exposures in Thailand date = 2011-06-28 keywords = Thailand; bat; exposure; rabies 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. doi = 10.1371/journal.pntd.0001054 id = cord-004510-cbutpjre author = Seetahal, Janine F. R. title = The Serological Prevalence of Rabies Virus-Neutralizing Antibodies in the Bat Population on the Caribbean Island of Trinidad date = 2020-02-05 keywords = RABV; RVNA; Rabies; Trinidad; bat 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. doi = 10.3390/v12020178 id = cord-270335-8vqi9c68 author = Seifert, Stephanie N title = Rousettus aegyptiacus Bats Do Not Support Productive Nipah Virus Replication date = 2019-11-04 keywords = EFB; Nipah; bat; virus 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] . doi = 10.1093/infdis/jiz429 id = cord-274241-biqbsggu author = Shaw, Timothy I. title = Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis) date = 2012-11-15 keywords = TCRV; bat; blast; gene; human; jamaican 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 ). doi = 10.1371/journal.pone.0048472 id = cord-338586-rkrkofri author = Shi, Zhengli title = Bat and virus date = 2010-02-01 keywords = bat 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) . doi = 10.1007/s13238-010-0029-7 id = cord-283756-ycjzitlk author = Simons, Robin R. L. title = Potential for Introduction of Bat-Borne Zoonotic Viruses into the EU: A Review date = 2014-05-16 keywords = Africa; Bangladesh; MARV; Nipah; bat; virus 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. doi = 10.3390/v6052084 id = cord-305024-343l2ha7 author = Sonntag, Michael title = New Adenovirus in Bats, Germany date = 2009-12-17 keywords = bat; dna 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. doi = 10.3201/eid1512.090646 id = cord-254543-gxwtqqdu author = Suwannarong, Kanokwan title = Bat consumption in Thailand date = 2016-01-22 keywords = Thailand; bat; guano 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. doi = 10.3402/iee.v6.29941 id = cord-313472-skcaw9ls author = Suwannarong, Kanokwan title = Risk factors for bat contact and consumption behaviors in Thailand; a quantitative study date = 2020-06-03 keywords = Thailand; bat 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) doi = 10.1186/s12889-020-08968-z id = cord-315972-5g2hnk1x author = Tong, Suxiang title = Detection of Novel SARS-like and Other Coronaviruses in Bats from Kenya date = 2009-03-17 keywords = SARS; bat 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. doi = 10.3201/eid1503.081013 id = cord-310061-nro623aa author = Valitutto, Marc T. title = Detection of novel coronaviruses in bats in Myanmar date = 2020-04-09 keywords = Myanmar; SARS; bat; sample 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] . doi = 10.1371/journal.pone.0230802 id = cord-347532-n51qv9pp author = Wacharapluesadee, Supaporn title = Group C Betacoronavirus in Bat Guano Fertilizer, Thailand date = 2013-08-17 keywords = RNA; bat 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 doi = 10.3201/eid1908.130119 id = cord-258160-v08cs51n author = Wang, Lin-Fa title = Review of Bats and SARS date = 2006-12-17 keywords = China; SARS; bat 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. doi = 10.3201/eid1212.060401 id = cord-270803-jtv5jmkn author = Wang, Lin-Fa title = Mass extinctions, biodiversity and mitochondrial function: are bats ‘special’ as reservoirs for emerging viruses? date = 2011-11-09 keywords = bat; host; rate; virus 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]. doi = 10.1016/j.coviro.2011.10.013 id = cord-277309-kelebqr6 author = Wang, Lin-Fa title = Viruses in bats and potential spillover to animals and humans date = 2019-01-18 keywords = Pteropus; SARS; bat; human; virus 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. doi = 10.1016/j.coviro.2018.12.007 id = cord-018821-e9oxvgar author = Webber, Quinn M. R. title = Sociality, Parasites, and Pathogens in Bats date = 2016-04-27 keywords = bat; host; parasite; social 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. doi = 10.1007/978-3-319-38953-0_5 id = cord-004502-3mkv3bal author = Wei, Gang 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 date = 2020-03-16 keywords = CMAP; Fig; HFD; NCD; PKA; UCP1; bat 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. doi = 10.1186/s12986-020-00440-4 id = cord-268645-5op2m7pu author = Wu, Zhiqiang title = Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases date = 2015-08-11 keywords = SARS; Supplementary; Table; bat; virus 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) . doi = 10.1038/ismej.2015.138 id = cord-276052-gk6n8slx author = Yadav, Pragya title = Isolation of Tioman virus from Pteropus giganteus bat in North-East region of India date = 2016-09-09 keywords = India; Pteropus; bat; virus 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. doi = 10.1016/j.meegid.2016.09.010 id = cord-255137-utg8k7qs author = Yinda, Claude Kwe title = Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses date = 2019-01-23 keywords = Cameroon; Fig; bat; cameroonian; human; strain; virus 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. doi = 10.1128/msphere.00585-18 id = cord-288451-npefpo3t author = Yinda, Claude Kwe title = Novel highly divergent reassortant bat rotaviruses in Cameroon, without evidence of zoonosis date = 2016-09-26 keywords = RVA; bat; strain; vp7 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. doi = 10.1038/srep34209 id = cord-289584-rbp7p8s9 author = Zhou, Ling title = Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China date = 2019-01-09 keywords = Bat; SADS 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) . doi = 10.1111/tbed.13008 id = cord-327534-f2wvh6la author = Zhou, Peng title = IRF7 in the Australian Black Flying Fox, Pteropus alecto: Evidence for a Unique Expression Pattern and Functional Conservation date = 2014-08-06 keywords = IFN; IRF3; IRF7; bat; figure 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 ). doi = 10.1371/journal.pone.0103875