Broad Host Range of SARS-Cov-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates
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Predicting Hosts Based on Early SARS-Cov-2 Samples And
www.nature.com/scientificreports OPEN Predicting hosts based on early SARS‑CoV‑2 samples and analyzing the 2020 pandemic Qian Guo1,2,3,7, Mo Li4,7, Chunhui Wang4,7, Jinyuan Guo1,3,7, Xiaoqing Jiang1,2,5,7, Jie Tan1, Shufang Wu1,2, Peihong Wang1, Tingting Xiao6, Man Zhou1,2, Zhencheng Fang1,2, Yonghong Xiao6* & Huaiqiu Zhu1,2,3,5* The SARS‑CoV‑2 pandemic has raised concerns in the identifcation of the hosts of the virus since the early stages of the outbreak. To address this problem, we proposed a deep learning method, DeepHoF, based on extracting viral genomic features automatically, to predict the host likelihood scores on fve host types, including plant, germ, invertebrate, non‑human vertebrate and human, for novel viruses. DeepHoF made up for the lack of an accurate tool, reaching a satisfactory AUC of 0.975 in the fve‑ classifcation, and could make a reliable prediction for the novel viruses without close neighbors in phylogeny. Additionally, to fll the gap in the efcient inference of host species for SARS‑CoV‑2 using existing tools, we conducted a deep analysis on the host likelihood profle calculated by DeepHoF. Using the isolates sequenced in the earliest stage of the COVID‑19 pandemic, we inferred that minks, bats, dogs and cats were potential hosts of SARS‑CoV‑2, while minks might be one of the most noteworthy hosts. Several genes of SARS‑CoV‑2 demonstrated their signifcance in determining the host range. Furthermore, a large‑scale genome analysis, based on DeepHoF’s computation for the later pandemic in 2020, disclosed the uniformity of host range among SARS‑CoV‑2 samples and the strong association of SARS‑CoV‑2 between humans and minks. -
Searching for Relatives of SARS-Cov-2 in Bats
RESEARCH HIGHLIGHTS IN BRIEF PUBLIC HEALTH Defeating dengue with Wolbachia The introduction of Wolbachia bacteria into Aedes aegypti mos- quitoes confers resistance to dengue virus (DENV) and other BROOK/ ROBERT Credit: LIBRARY/Alamy PHOTO SCIENCE arbovirues, and the release of Wolbachia- infected mosquitoes SYNTHETIC BIOLOGY in endemic regions may be an effective arboviral control strat- egy. Now, Utarini et al. report the results a cluster-randomized trial involving the release of A. aegypti mosquitoes infected with the wMel strain of Wolbachia pipientis for the control of DENV Designer bacteria infections in Yogyakarta, Indonesia. Geographical clusters ran- domly received either deployments of wMel- infected A. aegypti (interventional clusters) or no deployments (control clusters), Engineering bacteria by removing code of viral genomes. Cells were and virologically confirmed dengue (VCD) was surveyed in sense codons and their cognate treated with a cocktail of phages 8,144 patients from 18 primary care clinics. In the control clus- tRNAs could lead to the creation containing the phages lambda, ters, VCD occurred in 9.4% of patients but remarkably DENV of cells with desirable properties P1vir, T4, T6 and T7, which have was detected in only 2.3% of patients in interventional clusters. for biotechnology applications, such TCA or TCG sense codons that are The incidence of symptomatic dengue fever and hospitaliza- tions for VCD was significantly reduced in interventional clus- as complete resistance to contami- 10–58 times more abundant than the ters, suggesting that mosquito deployments could eliminate nating phages or the ability to incor- TAG codon in their genomes, and Ser dengue fever in endemic regions. -
Genome Organization of Canada Goose Coronavirus, a Novel
www.nature.com/scientificreports OPEN Genome Organization of Canada Goose Coronavirus, A Novel Species Identifed in a Mass Die-of of Received: 14 January 2019 Accepted: 25 March 2019 Canada Geese Published: xx xx xxxx Amber Papineau1,2, Yohannes Berhane1, Todd N. Wylie3,4, Kristine M. Wylie3,4, Samuel Sharpe5 & Oliver Lung 1,2 The complete genome of a novel coronavirus was sequenced directly from the cloacal swab of a Canada goose that perished in a die-of of Canada and Snow geese in Cambridge Bay, Nunavut, Canada. Comparative genomics and phylogenetic analysis indicate it is a new species of Gammacoronavirus, as it falls below the threshold of 90% amino acid similarity in the protein domains used to demarcate Coronaviridae. Additional features that distinguish the genome of Canada goose coronavirus include 6 novel ORFs, a partial duplication of the 4 gene and a presumptive change in the proteolytic processing of polyproteins 1a and 1ab. Viruses belonging to the Coronaviridae family have a single stranded positive sense RNA genome of 26–31 kb. Members of this family include both human pathogens, such as severe acute respiratory syn- drome virus (SARS-CoV)1, and animal pathogens, such as porcine epidemic diarrhea virus2. Currently, the International Committee on the Taxonomy of Viruses (ICTV) recognizes four genera in the Coronaviridae family: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. While the reser- voirs of the Alphacoronavirus and Betacoronavirus genera are believed to be bats, the Gammacoronavirus and Deltacoronavirus genera have been shown to spread primarily through birds3. Te frst three species of the Deltacoronavirus genus were discovered in 20094 and recent work has vastly expanded the Deltacoronavirus genus, adding seven additional species3. -
Supplementary Information
Supplementary Information This text file includes: Supplementary Methods Supplementary Figure 1-13, 15-30 Supplementary Table 1-8, 16, 20-21, 23, 25-37, 40-41 1 1. Samples, DNA extraction and genome sequencing 1.1 Ethical statements and sample storage The ethical statements of collecting and processing tissue samples for each species are listed as follows: Myotis myotis: All procedures were carried out in accordance with the ethical guidelines and permits (AREC-13-38-Teeling) delivered by the University College Dublin and the Préfet du Morbihan, awarded to Emma Teeling and Sébastien Puechmaille respectively. A single M. myotis individual was humanely sacrificed given that she had lethal injuries, and dissected. Rhinolophus ferrumequinum: All the procedures were conducted under the license (Natural England 2016-25216-SCI-SCI) issued to Gareth Jones. The individual bat died unexpectedly and suddenly during sampling and was dissected immediately. Pipistrellus kuhlii: The sampling procedure was carried out following all the applicable national guidelines for the care and use of animals. Sampling was done in accordance with all the relevant wildlife legislation and approved by the Ministry of Environment (Ministero della Tutela del Territorio e del Mare, Aut.Prot. N˚: 13040, 26/03/2014). Molossus molossus: All sampling methods were approved by the Ministerio de Ambiente de Panamá (SE/A-29-18) and by the Institutional Animal Care and Use Committee of the Smithsonian Tropical Research Institute (2017-0815-2020). Phyllostomus discolor: P. discolor bats originated from a breeding colony in the Department Biology II of the Ludwig-Maximilians-University in Munich. Approval to keep and breed the bats was issued by the Munich district veterinary office. -
The Rhinolophus Affinis Bat ACE2 and Multiple Animal Orthologs Are Functional 2 Receptors for Bat Coronavirus Ratg13 and SARS-Cov-2 3
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.16.385849; this version posted November 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 The Rhinolophus affinis bat ACE2 and multiple animal orthologs are functional 2 receptors for bat coronavirus RaTG13 and SARS-CoV-2 3 4 Pei Li1#, Ruixuan Guo1#, Yan Liu1#, Yintgtao Zhang2#, Jiaxin Hu1, Xiuyuan Ou1, Dan 5 Mi1, Ting Chen1, Zhixia Mu1, Yelin Han1, Zhewei Cui1, Leiliang Zhang3, Xinquan 6 Wang4, Zhiqiang Wu1*, Jianwei Wang1*, Qi Jin1*,, Zhaohui Qian1* 7 NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen 8 Biology, Chinese Academy of Medical Sciences and Peking Union Medical College1, 9 Beijing, 100176, China; School of Pharmaceutical Sciences, Peking University2, 10 Beijing, China; .Institute of Basic Medicine3, Shandong First Medical University & 11 Shandong Academy of Medical Sciences, Jinan 250062, Shandong, China; The 12 Ministry of Education Key Laboratory of Protein Science, Beijing Advanced 13 Innovation Center for Structural Biology, Beijing Frontier Research Center for 14 Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life 15 Sciences, Tsinghua University4, Beijing, China; 16 17 Keywords: SARS-CoV-2, bat coronavirus RaTG13, spike protein, Rhinolophus affinis 18 bat ACE2, host susceptibility, coronavirus entry 19 20 #These authors contributed equally to this work. 21 *To whom correspondence should be addressed: [email protected], 22 [email protected], [email protected], [email protected] 23 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.16.385849; this version posted November 17, 2020. -
Downloaded from the Genbank Database As of July 2020
viruses Article Modular Evolution of Coronavirus Genomes Yulia Vakulenko 1,2 , Andrei Deviatkin 3 , Jan Felix Drexler 1,4,5 and Alexander Lukashev 1,3,* 1 Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; [email protected] (Y.V.); [email protected] (J.F.D.) 2 Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia 3 Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; [email protected] 4 Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany 5 German Centre for Infection Research (DZIF), Associated Partner Site Charité, 10117 Berlin, Germany * Correspondence: [email protected] Abstract: The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and the extent of genetic divergence between partners, are scarce. Common methods of recombination detection based on phylogenetic incongruences (e.g., a phylogenetic com- patibility matrix) may fail in cases where too many events diminish the phylogenetic signal. Thus, an approach comparing genetic distances in distinct genome regions (pairwise distance deviation matrix) was set up. In alpha, beta, and delta-coronaviruses, a low incidence of recombination between closely related viruses was evident in all genome regions, but it was more extensive between the spike gene and other genome regions. -
Molecular Phylogeny of Mobatviruses (Hantaviridae) in Myanmar and Vietnam
viruses Article Molecular Phylogeny of Mobatviruses (Hantaviridae) in Myanmar and Vietnam Satoru Arai 1, Fuka Kikuchi 1,2, Saw Bawm 3 , Nguyễn Trường Sơn 4,5, Kyaw San Lin 6, Vương Tân Tú 4,5, Keita Aoki 1,7, Kimiyuki Tsuchiya 8, Keiko Tanaka-Taya 1, Shigeru Morikawa 9, Kazunori Oishi 1 and Richard Yanagihara 10,* 1 Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; [email protected] (S.A.); [email protected] (F.K.); [email protected] (K.A.); [email protected] (K.T.-T.); [email protected] (K.O.) 2 Department of Chemistry, Faculty of Science, Tokyo University of Science, Tokyo 162-8601, Japan 3 Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw 15013, Myanmar; [email protected] 4 Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam; [email protected] (N.T.S.); [email protected] (V.T.T.) 5 Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam 6 Department of Aquaculture and Aquatic Disease, University of Veterinary Science, Yezin, Nay Pyi Taw 15013, Myanmar; [email protected] 7 Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Tokyo 162-8601, Japan 8 Laboratory of Bioresources, Applied Biology Co., Ltd., Tokyo 107-0062, Japan; [email protected] 9 Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; [email protected] 10 Pacific Center for Emerging Infectious Diseases Research, John A. -
Acoustic Identification of Mormoopid Bats: a Survey During the Evening Exodus
Journal of Mammalogy, 87(2):324–330, 2006 ACOUSTIC IDENTIFICATION OF MORMOOPID BATS: A SURVEY DURING THE EVENING EXODUS SILVIO MACI´AS,* EMANUEL C. MORA, AND ADIANEZ GARCI´A Department of Human and Animal Biology, Faculty of Biology, Havana University, CP 10 400, Ciudad de La Habana, Cuba (SM, ECM, AG) Department of Basic Formation, Faculty of Psychology, Havana University, Calle San Rafael No. 1168 entre Mazo´n y Basarrate, Centro Habana, Ciudad de La Habana, Cuba (SM) Echolocation calls emitted by the 4 species of Cuban mormoopid bats were compared to determine vocal signatures that enable identification of each species in the field during their evening exodus. Echolocation calls produced by Mormoops blainvilli are downward frequency-modulated (FM) signals in the range of 68.4– 52.5 kHz. Echolocation calls emitted by Pteronotus macleayii and P. quadridens have a similar design consisting of a short constant-frequency (CF) segment followed by a downward FM segment. The CF segment was at 70.0 kHz in calls from P. macleayii, and at 83.3 kHz in calls from P. quadridens. Echolocation calls from P. parnellii consist of a long CF segment, which is preceded by a short initial upward sweep and followed by a downward FM terminal sweep. The CF value of the 2nd harmonic was a good parameter for species identification. The features of the echolocation calls of each of the species were used to identify them during the evening exodus from 2 Cuban caves. Key words: echolocation, evening exodus, identification, mormoopid bats Effective monitoring of echolocation calls is vital in many families, such as Mormoopidae, should make it possible to use studies of the ecology and conservation of bats (Fenton 1997). -
Exposure of Humans Or Animals to Sars-Cov-2 from Wild, Livestock, Companion and Aquatic Animals Qualitative Exposure Assessment
ISSN 0254-6019 Exposure of humans or animals to SARS-CoV-2 from wild, livestock, companion and aquatic animals Qualitative exposure assessment FAO ANIMAL PRODUCTION AND HEALTH / PAPER 181 FAO ANIMAL PRODUCTION AND HEALTH / PAPER 181 Exposure of humans or animals to SARS-CoV-2 from wild, livestock, companion and aquatic animals Qualitative exposure assessment Authors Ihab El Masry, Sophie von Dobschuetz, Ludovic Plee, Fairouz Larfaoui, Zhen Yang, Junxia Song, Wantanee Kalpravidh, Keith Sumption Food and Agriculture Organization for the United Nations (FAO), Rome, Italy Dirk Pfeiffer City University of Hong Kong, Hong Kong SAR, China Sharon Calvin Canadian Food Inspection Agency (CFIA), Science Branch, Animal Health Risk Assessment Unit, Ottawa, Canada Helen Roberts Department for Environment, Food and Rural Affairs (Defra), Equines, Pets and New and Emerging Diseases, Exotic Disease Control Team, London, United Kingdom of Great Britain and Northern Ireland Alessio Lorusso Istituto Zooprofilattico dell’Abruzzo e Molise, Teramo, Italy Casey Barton-Behravesh Centers for Disease Control and Prevention (CDC), One Health Office, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, United States of America Zengren Zheng China Animal Health and Epidemiology Centre (CAHEC), China Animal Health Risk Analysis Commission, Qingdao City, China Food and Agriculture Organization of the United Nations Rome, 2020 Required citation: El Masry, I., von Dobschuetz, S., Plee, L., Larfaoui, F., Yang, Z., Song, J., Pfeiffer, D., Calvin, S., Roberts, H., Lorusso, A., Barton-Behravesh, C., Zheng, Z., Kalpravidh, W. & Sumption, K. 2020. Exposure of humans or animals to SARS-CoV-2 from wild, livestock, companion and aquatic animals: Qualitative exposure assessment. FAO animal production and health, Paper 181. -
Noctilio Leporinus (Chiroptera, Noctilionidae) from South America
AMERICAN MUSEUM NOVITATES Number 3798, 31 pp. April 4, 2014 Quaternary Bats from the Impossível-Ioiô Cave System (Chapada Diamantina, Brazil): Humeral Remains and the First Fossil Record of Noctilio leporinus (Chiroptera, Noctilionidae) from South America LEANDRO O. SALLES,1, 2 JOAQUÍN ARROYO-CABRALES,3 ANNE CARULINY DO MONTE LIMA,1 WAGNER LANZELOTTI,1 FERNANDO A. PERINI,4 PAÚL M. VELAZCO,2 AND NANCY B. SIMMONS2 ABSTRACT The partially submerged Impossível-Ioiô cave system located in the karst region of Cha- pada Diamantina in Bahia (Brazil) has recently been the target of extensive paleontological studies. Here we provide the first report of fossil bats from this cave system, in which we rec- ognize six species based on humeral remains: Furipterus horrens, Chrotopterus auritus, Mor- moops cf. megalophylla, Pteronotus gymnonotus, Pteronotus parnellii, and Noctilio leporinus. Morphology of the humerus of these taxa is described in a comparative framework to docu- ment taxonomic assessments and provide a basis for future studies of fossil bat faunas. The relevance of the new records reported here is evaluated at a broader continental scale, as well as in contrast with the recent bat fauna of the region. The record of Noctilio leporinus stands as the first fossil occurrence of this species on the South American continent. 1 Mastozoologia, Departamento de Vertebrados, Museu Nacional/UFRJ, Quinta da Boa Vista, s/n, Rio de Janeiro 20940-040, Brazil. 2 Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History. 3 Laboratorio de Arqueozoología, Instituto Nacional de Antropología e Historia, Moneda # 16, Col. Centro México, D.F., México. 4 Departamento de Zoologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte 31270-901, Brazil. -
Cranial Morphology and Bite Force in Bats
CRANIOMANDIBULAR STRUCTURE AND FUNCTION IN MORMOOPID BATS A Thesis Presented to the faculty of the Department of Biological Sciences California State University, Sacramento Submitted in partial satisfaction of the requirements for the degree of MASTER OF SCIENCE in Biological Sciences by Jeffrey B. Changaris FALL 2017 © 2017 Jeffrey B. Changaris ALL RIGHTS RESERVED ii CRANIOMANDIBULAR STRUCTURE AND FUNCTION IN MORMOOPID BATS A Thesis by Jeffrey B. Changaris Approved by: ____________________________________, Committee Chair Dr. Ronald M. Coleman ____________________________________, Second Reader Dr. Winston C. Lancaster ____________________________________, Third Reader Dr. Joseph Bahlman ___________________________ Date iii Student: Jeffrey B. Changaris I certify that this student has met the requirements for format contained in the University format manual, and that this thesis is suitable for shelving in the Library and credit is to be awarded for the thesis. ____________________________, Graduate Coordinator _________________ Dr. James W. Baxter Date Department of Biological Sciences iv Abstract of CRANIOMANDIBULAR STRUCTURE AND FUNCTION IN MORMOOPID BATS by Jeffrey B. Changaris Neotropical Ghost-Faced bats of the genus Mormoops (Order Chiroptera, Family Mormoopidae) have a radically upturned rostrum, or snout, while the other mormoopid genus, Pteronotus, has only a slight upturning of the rostrum. This type of difference in morphology between closely related taxa is likely to be the result of some sort of specialization. Observation of Mormoops blainvillei, the Antillean Ghost-Faced bat, reveals that they can open their mouths very wide relative to the size of their heads. Mormoopid bats are insectivorous with Mormoops blainvillei having a prey preference of large moths, but related species, such as Pteronotus quadridens, the Sooty Mustached bat, have a more varied diet with a large component of smaller hard-bodied beetles. -
Ebola, KFD and Bats
Journal of Communicable Diseases Volume 51, Issue 4 - 2019, Pg. No. 69-72 Peer Reviewed & Open Access Journal Review Article Ebola, KFD and Bats PK Rajagopalan Former Director, Vector Control Research Center, Indian Council of Medical Research and formerly: WHO STAC Member, WHO Consultant and WHO Expert Committee Member on Malaria, Filariasis and Vector Control. DOI: https://doi.org/10.24321/0019.5138.201939 INFO ABSTRACT E-mail Id: The headline in the Times of India, dated July 23, 2019, “India Needs [email protected] to Prepare for Ebola, Other Viral Diseases” was frightening. It quotes Orcid Id: an article in Indian Journal of Medical Research, which states “Bats https://orcid.org/0000-0002-8324-3096 are thought to be the natural reservoirs of this virus…..India is home How to cite this article: to a great diversity of bat species….” But Ebola has not yet come to Rajagopalan PK. Ebola, KFD and Bats. J Commun India, though there is every possibility. But what about Kyasanur Forest Dis 2019; 51(4): 69-72. Disease (KFD), which is already in India and which has links with an insectivorous bat? Recognized in 1957, the virus was isolated in 1969 Date of Submission: 2019-08-22 over fifty years ago from four insectivorous bats, Rhinolophus rouxii, Date of Acceptance: 2019-12-23 and from Ornithodoros ticks collected from the roosting habitat of these bats, (Ind. J. Med. Res, 1969, 905-8). KFD came as a big enough epidemic in 1957, but later petered out and then sporadically appeared throughout the Western Ghat region, from Kerala to Gujarat and an epidemic resurfacing in the oldest theater in January 2019! There were many publications in India about investigations done in these areas, but none of them mentioned anything about bats.