Supplementary Figure 1 – Contour Plot of Oc43 and Homologues in Animals
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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. -
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. -
Broad Receptor Engagement of an Emerging Global Coronavirus May Potentiate Its Diverse Cross-Species Transmissibility
Broad receptor engagement of an emerging global coronavirus may potentiate its diverse cross-species transmissibility Wentao Lia,1, Ruben J. G. Hulswita,1, Scott P. Kenneyb,1, Ivy Widjajaa, Kwonil Jungb, Moyasar A. Alhamob, Brenda van Dierena, Frank J. M. van Kuppevelda, Linda J. Saifb,2, and Berend-Jan Boscha,2 aVirology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; and bDepartment of Veterinary Preventive Medicine, Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691 Contributed by Linda J. Saif, April 12, 2018 (sent for review February 15, 2018; reviewed by Tom Gallagher and Stefan Pöhlmann) Porcine deltacoronavirus (PDCoV), identified in 2012, is a common greatly increase the potential for successful adaptation to a new enteropathogen of swine with worldwide distribution. The source host (6, 12). A pivotal criterion of cross-species transmission and evolutionary history of this virus is, however, unknown. concerns the ability of a virus to engage a receptor within the PDCoV belongs to the Deltacoronavirus genus that comprises pre- novel host, which for CoVs, is determined by the receptor dominantly avian CoV. Phylogenetic analysis suggests that PDCoV specificity of the viral spike (S) entry protein. originated relatively recently from a host-switching event be- The porcine deltacoronavirus (PDCoV) is a recently discov- tween birds and mammals. Insight into receptor engagement by ered CoV of unknown origin. PDCoV (species name coronavirus PDCoV may shed light into such an exceptional phenomenon. Here HKU15) was identified in Hong Kong in pigs in the late 2000s we report that PDCoV employs host aminopeptidase N (APN) as an (13) and has since been detected in swine populations in various entry receptor and interacts with APN via domain B of its spike (S) countries worldwide (14–24). -
Canine Coronaviruses: Emerging and Re-Emerging Pathogens of Dogs
1 Berliner und Münchener Tierärztliche Wochenschrift 2021 (134) Institute of Animal Hygiene and Veterinary Public Health, University Leipzig, Open Access Leipzig, Germany Berl Münch Tierärztl Wochenschr (134) 1–6 (2021) Canine coronaviruses: emerging and DOI 10.2376/1439-0299-2021-1 re-emerging pathogens of dogs © 2021 Schlütersche Fachmedien GmbH Ein Unternehmen der Schlüterschen Canine Coronaviren: Neu und erneut auftretende Pathogene Mediengruppe des Hundes ISSN 1439-0299 Korrespondenzadresse: Ahmed Abd El Wahed, Uwe Truyen [email protected] Eingegangen: 08.01.2021 Angenommen: 01.04.2021 Veröffentlicht: 29.04.2021 https://www.vetline.de/berliner-und- muenchener-tieraerztliche-wochenschrift- open-access Summary Canine coronavirus (CCoV) and canine respiratory coronavirus (CRCoV) are highly infectious viruses of dogs classified as Alphacoronavirus and Betacoronavirus, respectively. Both are examples for viruses causing emerging diseases since CCoV originated from a Feline coronavirus-like Alphacoronavirus and CRCoV from a Bovine coronavirus-like Betacoronavirus. In this review article, differences in the genetic organization of CCoV and CRCoV as well as their relation to other coronaviruses are discussed. Clinical pictures varying from an asymptomatic or mild unspecific disease, to respiratory or even an acute generalized illness are reported. The possible role of dogs in the spread of the Betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial to study as ani- mal always played the role of establishing zoonotic diseases in the community. Keywords: canine coronavirus, canine respiratory coronavirus, SARS-CoV-2, genetics, infectious diseases Zusammenfassung Das canine Coronavirus (CCoV) und das canine respiratorische Coronavirus (CRCoV) sind hochinfektiöse Viren von Hunden, die als Alphacoronavirus bzw. -
On the Coronaviruses and Their Associations with the Aquatic Environment and Wastewater
water Review On the Coronaviruses and Their Associations with the Aquatic Environment and Wastewater Adrian Wartecki 1 and Piotr Rzymski 2,* 1 Faculty of Medicine, Poznan University of Medical Sciences, 60-812 Pozna´n,Poland; [email protected] 2 Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Pozna´n,Poland * Correspondence: [email protected] Received: 24 April 2020; Accepted: 2 June 2020; Published: 4 June 2020 Abstract: The outbreak of Coronavirus Disease 2019 (COVID-19), a severe respiratory disease caused by betacoronavirus SARS-CoV-2, in 2019 that further developed into a pandemic has received an unprecedented response from the scientific community and sparked a general research interest into the biology and ecology of Coronaviridae, a family of positive-sense single-stranded RNA viruses. Aquatic environments, lakes, rivers and ponds, are important habitats for bats and birds, which are hosts for various coronavirus species and strains and which shed viral particles in their feces. It is therefore of high interest to fully explore the role that aquatic environments may play in coronavirus spread, including cross-species transmissions. Besides the respiratory tract, coronaviruses pathogenic to humans can also infect the digestive system and be subsequently defecated. Considering this, it is pivotal to understand whether wastewater can play a role in their dissemination, particularly in areas with poor sanitation. This review provides an overview of the taxonomy, molecular biology, natural reservoirs and pathogenicity of coronaviruses; outlines their potential to survive in aquatic environments and wastewater; and demonstrates their association with aquatic biota, mainly waterfowl. It also calls for further, interdisciplinary research in the field of aquatic virology to explore the potential hotspots of coronaviruses in the aquatic environment and the routes through which they may enter it. -
Hydroxychloroquine Or Chloroquine for Treating Coronavirus Disease 2019 (COVID-19) – a PROTOCOL for a Systematic Review of Individual Participant Data
Hydroxychloroquine or Chloroquine for treating Coronavirus Disease 2019 (COVID-19) – a PROTOCOL for a systematic review of Individual Participant Data Authors Fontes LE, Riera R, Miranda E, Oke J, Heneghan CJ, Aronson JK, Pacheco RL, Martimbianco ALC, Nunan D BACKGROUND In the face of the pandemic of SARS CoV2, urgent research is needed to test potential therapeutic agents against the disease. Reliable research shall inform clinical decision makers. Currently, there are several studies testing the efficacy and safety profiles of different pharmacological interventions. Among these drugs, we can cite antimalarial, antivirals, biological drugs, interferon, etc. As of 6 April 2020 there are three published reportsand 100 ongoing trials testing hydroxychloroquine/chloroquine alone or in association with other drugs for COVID-19. This prospective systematic review with Individual Participant data aims to assess the rigour of the best-available evidence for hydroxychloroquine or chloroquine as treatment for COVID-19 infection. The PICO framework is: P: adults with COVID-19 infection I: chloroquine or hydroxychloroquine (alone or in association) C: placebo, other active treatments, usual standard care without antimalarials O: efficacy and safety outcomes OBJECTIVES To assess the effects (benefits and harms) of chloroquine or hydroxychloroquine for the treatment of COVID-19 infection. METHODS Criteria for considering studies for this review Types of studies We shall include randomized controlled trials (RCTs) with a parallel design. We intend to include even small trials (<50 participants), facing the urgent need for evidence to respond to the current pandemic. Quasi-randomized, non-randomized, or observational studies will be excluded due to a higher risk of confounding and selection bias (1). -
Immune Evasion of SARS-Cov-2 Emerging Variants: What Have We Learnt So Far?
viruses Review Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Ivana Lazarevic * , Vera Pravica, Danijela Miljanovic and Maja Cupic Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; [email protected] (V.P.); [email protected] (D.M.); [email protected] (M.C.) * Correspondence: [email protected]; Tel.: +381-11-3643-379 Abstract: Despite the slow evolutionary rate of SARS-CoV-2 relative to other RNA viruses, its massive and rapid transmission during the COVID-19 pandemic has enabled it to acquire significant genetic diversity since it first entered the human population. This led to the emergence of numerous variants, some of them recently being labeled “variants of concern” (VOC), due to their potential impact on transmission, morbidity/mortality, and the evasion of neutralization by antibodies elicited by infection, vaccination, or therapeutic application. The potential to evade neutralization is the result of diversity of the target epitopes generated by the accumulation of mutations in the spike protein. While three globally recognized VOCs (Alpha or B.1.1.7, Beta or B.1.351, and Gamma or P.1) remain sensitive to neutralization albeit at reduced levels by the sera of convalescent individuals and recipients of several anti-COVID19 vaccines, the effect of spike variability is much more evident on the neutralization capacity of monoclonal antibodies. The newly recognized VOC Delta or lineage B.1.617.2, as well as locally accepted VOCs (Epsilon or B.1.427/29-US and B1.1.7 with the E484K-UK) are indicating the necessity of close monitoring of new variants on a global level. -
Coronaviruses: a Review of Their Properties and Diversity
Properties and diversity of coronaviruses Afr. J. Clin. Exper. Microbiol. 2020; 21 (4): 258-271 Joseph and Fagbami. Afr. J. Clin. Exper. Microbiol. 2020; 21 (4): 258 - 271 https://www.afrjcem.org African Journal of Clinical and Experimental Microbiology. ISSN 1595-689X Oct 2020; Vol.21 No.4 AJCEM/2038. https://www.ajol.info/index.php/ajcem Copyright AJCEM 2020: https://doi.org/10.4314/ajcem.v21i4.2 Review Article Open Access Coronaviruses: a review of their properties and diversity Joseph, A. A., and *Fagbami, A. H. Department of Microbial Pathology, Faculty of Basic Clinical Sciences, University of Medical Sciences, Ondo, Nigeria *Correspondence to: [email protected] Abstract: Human coronaviruses, which hitherto were causative agents of mild respiratory diseases of man, have recently become one of the most important groups of pathogens of humans the world over. In less than two decades, three members of the group, severe acute respiratory syndrome (SARS) coronavirus (CoV), Middle East respiratory syndrome (MERS)-CoV, and SARS-COV-2, have emerged causing disease outbreaks that affected millions and claimed the lives of thousands of people. In 2017, another coronavirus, the swine acute diarrhea syndrome (SADS) coronavirus (SADS-CoV) emerged in animals killing over 24,000 piglets in China. Because of the medical and veterinary importance of coronaviruses, we carried out a review of available literature and summarized the current information on their properties and diversity. Coronaviruses are single-stranded RNA viruses with some unique characteristics such as the possession of a very large nucleic acid, high infidelity of the RNA-dependent polymerase, and high rate of mutation and recombination in the genome. -
SARS-Cov-2 Surveillance in Norway Rats (Rattus Norvegicus) from Antwerp Sewer System
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.06.433708; this version posted March 6, 2021. 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-ND 4.0 International license. 1 SARS-CoV-2 surveillance in Norway rats (Rattus norvegicus) from Antwerp sewer system, 2 Belgium 3 Valeria Carolina Colombo 1,2, Vincent Sluydts1, Joachim Mariën1,3, Bram Vanden Broecke1, Natalie 4 Van Houtte1, Wannes Leirs1, Lotte Jacobs4, Arne Iserbyt1, Marine Hubert1, Leo Heyndrickx3, Hanne 5 Goris1, Peter Delputte4, Naomi De Roeck4, Joris Elst1, Robbert Boudewijns5, Kevin K. Ariën3, Herwig 6 Leirs1, Sophie Gryseels1,6 7 1. Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium 8 2. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina 9 3. Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, 10 Belgium 11 4. Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, 12 Belgium 13 5. Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, 14 Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, 15 Belgium 16 6. OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium 17 Abstract 18 Background 19 SARS-CoV-2 human-to-animal transmission can lead to the establishment of novel reservoirs and 20 the evolution of new variants with the potential to start new outbreaks in humans. 21 Aim bioRxiv preprint doi: https://doi.org/10.1101/2021.03.06.433708; this version posted March 6, 2021. -
Complete Sections As Applicable
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2010.023a-dV officers) Short title: A new genus and three new species in the subfamily Coronavirinae (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Raoul J. de Groot and Alexander E. Gorbalenya List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . If Submission on behalf of the Coronavirus Study in doubt, contact the appropriate subcommittee Group. Authors are CSG members (R.J de chair (fungal, invertebrate, plant, prokaryote or Groot, Chair) vertebrate viruses) ICTV-EC or Study Group comments and response of the proposer: Date first submitted to ICTV: Date of this revision (if different to above): Page 1 of 5 MODULE 2: NEW SPECIES Code 2010.023aV (assigned by ICTV officers) To create new species within: Genus: Deltacoronavirus (new) Subfamily: Coronavirinae Family: Coronaviridae Order: Nidovirales And name the new species: GenBank sequence accession number(s) of reference isolate: Bulbul coronavirus HKU11 [FJ376619] Thrush coronavirus HKU12 [FJ376621=NC_011549] Munia coronavirus HKU13 [FJ376622=NC_011550] Reasons to justify the creation and assignment of the new species: According to the demarcation criteria as outlined in Module 3 and agreed upon by the Coronavirus Study Group, the new coronaviruses isolated from Bulbul, Thrush and Munia are representatives of separates species.