DOCSLIB.ORG

Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-Cov-2 Phylogeny and Risk Assessment for Future Outbreaks †

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-Cov-2 Phylogeny and Risk Assessment for Future Outbreaks † biomolecules Editorial Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for Future Outbreaks † Murat Seyran 1, Sk. Sarif Hassan 2 , Vladimir N. Uversky 3,* , Pabitra Pal Choudhury 4, Bruce D. Uhal 5 , Kenneth Lundstrom 6,*, Diksha Attrish 7, Nima Rezaei 8,9, Alaa A. A. Aljabali 10 , Shinjini Ghosh 11, Damiano Pizzol 12 , Parise Adadi 13 , Tarek Mohamed Abd El-Aziz 14,15 , Ramesh Kandimalla 16, Murtaza M. Tambuwala 17 , Amos Lal 18, Gajendra Kumar Azad 19 , Samendra P. Sherchan 20, Wagner Baetas-da-Cruz 21 , Giorgio Palù 22,* and Adam M. Brufsky 23 1 Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Währinger Straße, A-1090 Vienna, Austria; [email protected] 2 Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India; [email protected] 3 Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA 4 Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India; [email protected] 5 Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; [email protected] 6 PanTherapeutics, Rte de Lavaux 49, CH1095 Lutry, Switzerland 7 Dr. B R Ambedkar Center for Biomedical Research (ACBR), University of Delhi (North Camps), Delhi-110007, India; [email protected] 8 Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran, Citation: Seyran, M.; Hassan, S..S.; University of Medical Sciences, Tehran 1419733151, Iran; [email protected] Uversky, V.N.; Pal Choudhury, P.; 9 Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education Uhal, B.D.; Lundstrom, K.; Attrish, D.; and Research Network (USERN), Tehran 1419733151, Iran Rezaei, N.; Aljabali, A.A.A.; Ghosh, S.; 10 Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, et al. Urgent Need for Field Surveys Irbid 566, Jordan; [email protected] 11 of Coronaviruses in Southeast Asia to Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Understand the SARS-CoV-2 Kolkata 700009, West Bengal, India; [email protected] 12 Phylogeny and Risk Assessment for Italian Agency for Development Cooperation—Khartoum, Sudan Street 33, Al Amarat 13374, Sudan; [email protected] Future Outbreaks . Biomolecules 2021, 13 Department of Food Science, University of Otago, Dunedin 9054, New Zealand; [email protected] 11, 398. https://doi.org/10.3390/ 14 Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, biom11030398 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA; [email protected] 15 Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt Received: 10 January 2021 16 CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Accepted: 20 February 2021 Hyderabad 500007, Telangana State, India; [email protected] Published: 9 March 2021 17 School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK; [email protected] 18 Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN 55905, USA; Publisher’s Note: MDPI stays neutral [email protected] with regard to jurisdictional claims in 19 Department of Zoology, Patna University, Patna 800005, Bihar, India; [email protected] published maps and institutional affil- 20 Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA; iations. [email protected] 21 Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941901, Brazil; [email protected] 22 Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy 23 UPMC Hillman Cancer Center, Department of Medicine, Division of Hematology/Oncology, University of Copyright: © 2021 by the authors. Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; [email protected] Licensee MDPI, Basel, Switzerland. * Correspondence: [email protected] (V.N.U.); [email protected] (K.L.); [email protected] (G.P.) This article is an open access article † All authors are the members of the Self-Assembled COVID Research and Education Directive distributed under the terms and (SACRED) Consortium. conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS- 4.0/). CoV-2) is focused on a single isolate of bat coronaviruses (bat CoVs) which does not Biomolecules 2021, 11, 398. https://doi.org/10.3390/biom11030398 https://www.mdpi.com/journal/biomolecules Biomolecules 2021, 11, x FOR PEER REVIEW 2 of 7 Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) is focused on a single isolate of bat coronaviruses (bat CoVs) which does not ade- Biomolecules 2021, 11, 398 2 of 7 quately represent genetically related coronaviruses (CoVs). The unique bat CoV RaTG13 is the only identified sequence genetically associated with SARS-CoV-2. Data scarcity of bat CoV sequences raises concerns over several fundamental experimental and biostatis- adequatelytical aspects, represent e.g., repeatability genetically related of sequences coronaviruses and (CoVs). intraspecies The unique variations bat CoV RaTG13in critical gene is the only identified sequence genetically associated with SARS-CoV-2. Data scarcity of bat regions, such as the receptor-binding domain of the spike protein. The Sunda pangolin CoV sequences raises concerns over several fundamental experimental and biostatistical aspects,has been e.g., proposed repeatability as the of sequencesintermediate and intraspecieshost and source variations of SARS-CoV-2, in critical gene but regions, no pangolin suchCoV asisolates the receptor-binding have been reported domain ofin theits spikehabitats protein. in Southeast The Sunda Asia. pangolin Most has pangolin been CoVs proposedwere isolated as the from intermediate pangolins host captured and source during of SARS-CoV-2, illegal animal but no trafficking, pangolin CoV raising isolates questions haveabout been such reported isolates’ in reliability its habitats and in Southeast quality. Problems Asia. Most with pangolin pangolin CoVs CoV were sampling isolated are also fromrelated pangolins to the capturedsubstandard during quality illegal of animal deposite trafficking,d sequences. raising There questions is an about urgent such need for isolates’field surveys reliability of bat and CoVs quality. and Problems possible with intermediate pangolin CoV hosts, sampling such as are pangolins, also related ferrets, to and thecivets, substandard in Southeast quality Asia of depositedto investigate sequences. the genomic There is source an urgent of SARS-CoV-2 need for field surveysand assess pos- of bat CoVs and possible intermediate hosts, such as pangolins, ferrets, and civets, in sible future risks for new outbreaks. Southeast Asia to investigate the genomic source of SARS-CoV-2 and assess possible future risks forSARS-CoV-2 new outbreaks. is the causative agent of the coronavirus disease 2019 (COVID-19) pan- demicSARS-CoV-2 in which isthe the first causative cases agentwere of reported the coronavirus in Wuhan, disease Hubei 2019 (COVID-19)Province, China. pan- SARS- demicCoV-2, in a whichmember the of first Betacoronavirus cases were reported and subgenus in Wuhan, Sarbecovirus Hubei Province,, is phylogenetically China. SARS- related CoV-2,to bat acoronaviruses member of Betacoronavirus (bat CoVs)and RaTG13 subgenus (detectedSarbecovirus in Pu’er, is phylogenetically City in 2013) related and RmYN02 to(detected bat coronaviruses in Xishuangbanna (bat CoVs) City RaTG13 in 2019) (detected and were in Pu’er detected City inapproximately 2013) and RmYN02 2000 km from (detectedWuhan [1,2]. in Xishuangbanna Betacoronavirus City and in 2019) its genetic and were reservoir detected bat approximately species, such 2000 as kmthe fromintermediate Wuhanhorseshoe [1,2]. batBetacoronavirus Rhinolophusand affinis its genetic, inhabit reservoir Southeast bat species,Asia [1,3,4 such]. as It thehas intermediate been hypothesized horseshoe bat Rhinolophus affinis, inhabit Southeast Asia [1,3,4]. It has been hypothesized that pangolin CoVs may have originated from cross-species transmission in bats [5]. To that pangolin CoVs may have originated from cross-species transmission in bats [5]. To date,date, no no additional additional bat bat CoVs CoVs RaTG13 RaTG13 or RmYN02 or RmYN02 isolates isolates and no and pangolin no pangolin CoV isolates CoV isolates originatingoriginating from from healthy healthy or sickor sick pangolins pangolins in their in their natural natural habitats habitats in Southeast in Southeast Asian Asian countriescountries have have been been sequenced sequenced (Figure (Figure1). Therefore, 1). Ther here,efore, we here, seek towe draw seek the to attentiondraw the of attention relevantof relevant institutions institutions toward toward the need the to need obtain to CoVobtain isolates CoV fromisolates potential from hosts,potential such hosts, as such healthyas healthy or sick or pangolins,sick pangolins, in their in natural their natura habitatsl habitats to
Load more

Recommended publications
  • Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-Cov-2 Spike Glycoprotein Increased Correlated Dynamic Movements
    International Journal of Molecular Sciences Article Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements Massimiliano S. Tagliamonte 1,2,† , Nabil Abid 3,4,†, Stefano Borocci 5,6 , Elisa Sangiovanni 5, David A. Ostrov 2 , Sergei L. Kosakovsky Pond 7, Marco Salemi 1,2,*, Giovanni Chillemi 5,8,*,‡ and Carla Mavian 1,2,*,‡ 1 Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA; mstagliamonte@ufl.edu 2 Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; [email protected]fl.edu 3 Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, 5000 Monastir, Tunisia; [email protected] 4 Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia 5 Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; [email protected] (S.B.); [email protected] (E.S.) 6 Institute for Biological Systems, National Research Council, Via Salaria, Km 29.500, 00015 Monterotondo, Rome, Italy 7 Department of Biology, Temple University, Philadelphia, PA 19122, USA; [email protected] 8 Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola, 122/O, 70126 Bari, Italy * Correspondence: [email protected]fl.edu (M.S.); [email protected] (G.C.); cmavian@ufl.edu (C.M.) † Authors contributed equally as first to this work. ‡ Authors contributed equally as last to this work.
    [Show full text]
  • Inverted Repeats in Coronavirus SARS-Cov-2 Genome and Implications in Evolution
    Inverted repeats in coronavirus SARS-CoV-2 genome and implications in evolution Changchuan Yin ID ∗ Department of Mathematics, Statistics, and Computer Science University of Illinois at Chicago Chicago, IL 60607 USA Stephen S.-T. Yau ID y Department of Mathematical Sciences Tsinghua University Beijing 100084 China Abstract The coronavirus disease (COVID-19) pandemic, caused by the coronavirus SARS- CoV-2, has caused 60 millions of infections and 1.38 millions of fatalities. Genomic analysis of SARS-CoV-2 can provide insights on drug design and vaccine develop- ment for controlling the pandemic. Inverted repeats in a genome greatly impact the stability of the genome structure and regulate gene expression. Inverted repeats involve cellular evolution and genetic diversity, genome arrangements, and diseases. Here, we investigate the inverted repeats in the coronavirus SARS-CoV-2 genome. We found that SARS-CoV-2 genome has an abundance of inverted repeats. The inverted repeats are mainly located in the gene of the Spike protein. This result suggests the Spike protein gene undergoes recombination events, therefore, is essential for fast evolution. Comparison of the inverted repeat signatures in human and bat coronaviruses suggest that SARS-CoV-2 is mostly related SARS-related coronavirus, SARSr-CoV/RaTG13. The study also reveals that the recent SARS- related coronavirus, SARSr-CoV/RmYN02, has a high amount of inverted repeats in the spike protein gene. Besides, this study demonstrates that the inverted repeat distribution in a genome can be considered as the genomic signature. This study highlights the significance of inverted repeats in the evolution of SARS-CoV-2 and presents the inverted repeats as the genomic signature in genome analysis.
    [Show full text]
  • Exploring the Natural Origins of SARS-Cov-2
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.22.427830; this version posted January 22, 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 4.0 International license. Exploring the natural origins of SARS-CoV-2 1 1 2 3 1,* Spyros Lytras ,​ Joseph Hughes ,​ Wei Xia ,​ Xiaowei Jiang ,​ David L Robertson ​ ​ ​ ​ ​ 1 MRC-University​ of Glasgow Centre for Virus Research (CVR), Glasgow, UK. 2 National​ School of Agricultural Institution and Development, South China Agricultural University, Guangzhou, China. 3 Department​ of Biological Sciences, Xi'an Jiaotong-Liverpool University (XJTLU), Suzhou, China. * Correspondence:​ [email protected] Summary. The lack of an identifiable intermediate host species for the proximal animal ​ ancestor of SARS-CoV-2 and the distance (~1500 km) from Wuhan to Yunnan province, where the closest evolutionary related coronaviruses circulating in horseshoe bats have been identified, is fueling speculation on the natural origins of SARS-CoV-2. Here we analyse SARS-CoV-2’s related horseshoe bat and pangolin Sarbecoviruses and confirm ​ Rhinolophus affinis continues to be the likely reservoir species as its host range extends ​ across Central and Southern China. This would explain the bat Sarbecovirus recombinants ​ in the West and East China, trafficked pangolin infections and bat Sarbecovirus recombinants linked to Southern China. Recent ecological disturbances as a result of changes in meat consumption could then explain SARS-CoV-2 transmission to humans through direct or indirect contact with the reservoir wildlife, and subsequent emergence towards Hubei in Central China.
    [Show full text]
  • WHO-Convened Global Study of Origins of SARS-Cov-2: China Part
    WHO-convened Global Study of Origins of SARS-CoV-2: China Part Joint WHO-China Study 14 January-10 February 2021 Joint Report 1 LIST OF ABBREVIATIONS AND ACRONYMS ARI acute respiratory illness cDNA complementary DNA China CDC Chinese Center for Disease Control and Prevention CNCB China National Center for Bioinformation CoV coronavirus Ct values cycle threshold values DDBJ DNA Database of Japan EMBL-EBI European Molecular Biology Laboratory and European Bioinformatics Institute FAO Food and Agriculture Organization of the United Nations GISAID Global Initiative on Sharing Avian Influenza Database GOARN Global Outbreak Alert and Response Network Hong Kong SAR Hong Kong Special Administrative Region Huanan market Huanan Seafood Wholesale Market IHR International Health Regulations (2005) ILI influenza-like illness INSD International Nucleotide Sequence Database MERS Middle East respiratory syndrome MRCA most recent common ancestor NAT nucleic acid testing NCBI National Center for Biotechnology Information NMDC National Microbiology Data Center NNDRS National Notifiable Disease Reporting System OIE World Organisation for Animal Health (Office international des Epizooties) PCR polymerase chain reaction PHEIC public health emergency of international concern RT-PCR real-time polymerase chain reaction SARI severe acute respiratory illness SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 SARSr-CoV-2 Severe acute respiratory syndrome coronavirus 2-related virus tMRCA time to most recent common ancestor WHO World Health Organization WIV Wuhan Institute of Virology 2 Acknowledgements WHO gratefully acknowledges the work of the joint team, including Chinese and international scientists and WHO experts who worked on the technical sections of this report, and those who worked on studies to prepare data and information for the joint mission.
    [Show full text]
  • Science Journals
    RESEARCH CORONAVIRUS ticles showed enhanced heterologous binding and neutralization properties against hu- Mosaic nanoparticles elicit cross-reactive immune man and bat SARS-like betacoronaviruses (sarbecoviruses). responses to zoonotic coronaviruses in mice We used a study of sarbecovirus RBD re- ceptor usage and cell tropism (38) to guide Alexander A. Cohen1, Priyanthi N. P. Gnanapragasam1, Yu E. Lee1, Pauline R. Hoffman1, Susan Ou1, our choice of RBDs for co-display on mosaic Leesa M. Kakutani1, Jennifer R. Keeffe1, Hung-Jen Wu2, Mark Howarth2, Anthony P. West1, particles. From 29 RBDs that were classified Christopher O. Barnes1, Michel C. Nussenzweig3, Pamela J. Bjorkman1* into distinct clades (clades 1, 2, 1/2, and 3) (38), we identified diverse RBDs from SARS- Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-related emergent CoV, WIV1, and SHC014 (clade 1); SARS-CoV-2 zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor binding (clade 1/2); Rs4081, Yunnan 2011 (Yun11), and domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses Rf1 (clade 2); and BM-4831 (clade 3). Of these, that represent threats to humans (mosaic nanoparticles with four to eight distinct RBDs). Mice immunized SARS-CoV-2 and SARS-CoV are human coro- with RBD nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. naviruses and the rest are bat viruses originat- Mosaic RBD nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs ing in China or Bulgaria (BM-4831). We also relative to sera from immunizations with homotypic SARS-CoV-2–RBD nanoparticles or COVID-19 convalescent included RBDs from the GX pangolin clade 1/2 human plasmas.
    [Show full text]
  • The SARS-Cov-2 Arginine Dimers
    The SARS-CoV-2 arginine dimers Antonio R. Romeu ( [email protected] ) University Rovira i Virgili Enric Ollé University Rovira i Virgili Short Report Keywords: SARS-CoV-2, Sarbecovirus, Arginine dimer, Arginine codons usage, Bioinformatics Posted Date: August 2nd, 2021 DOI: https://doi.org/10.21203/rs.3.rs-770380/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License The SARS-CoV-2 arginine dimers Antonio R. Romeu1 and Enric Ollé2 1: Chemist. Professor of Biochemistry and Molecular Biology. University Rovira i Virgili. Tarragona. Spain. Corresponding author. Email: [email protected] 2: Veterinarian, Biochemist. Associate Professor of the Department of Biochemistry and Biotechnology. University Rovira i Virgili. Tarragona. Spain. Email: [email protected] Abstract Arginine is present, even as a dimer, in the viral polybasic furin cleavage sites, including that of SARS-CoV-2 in its protein S, whose acquisition is one of its characteristics that distinguishes it from the rest of the sarbecoviruses. The CGGCGG sequence encodes the SARS-CoV-2 furin site RR dimer. The aim of this work is to report the other SARS-CoV-2 arginine pairs, with particular emphasis in their codon usage. Here we show the presence of RR dimers in the orf1ab related non structural proteins nsp3, nsp4, nsp6, nsp13 and nsp14A2. Also, with a higher proportion in the structural roteinp nucleocapsid. All these RR dimers were strictly conserved in the sarbecovirus strains closest to SARS-CoV-2, and none of them was encoded by the CGGCGG sequence. Key words SARS-CoV-2, Sarbecovirus, Arginine dimer, Arginine codons usage, Bioinformatics Introduction Arginine (R) is a polar and non-hydrophobic amino acid, with a positive charged guanidine group, a physiological pH, linked a 3-hydrocarbon aliphatic chain.
    [Show full text]
  • To Stop the Next Pandemic, We Need to Unravel the Origins of COVID-19 David A
    OPINION OPINION To stop the next pandemic, we need to unravel the origins of COVID-19 David A. Relmana,b,c,d,1 We find ourselves ten months into one of the most to have been collected from bats in 2013 and 2019, catastrophic global health events of our lifetime and, respectively, in Yunnan Province, China (1). COVID-19 disturbingly, we still do not know how it began. What’s was first reported in December 2019 more than 1,000 even more troubling is that despite the critical impor- miles away in Wuhan City, Hubei Province, China. tance of this question, efforts to investigate the origins Beyond these facts, the “origin story” is missing many of the severe acute respiratory syndrome coronavirus key details, including a plausible and suitably detailed 2 (SARS-CoV-2) virus and of the associated disease, recent evolutionary history of the virus, the identity coronavirus disease 2019 (COVID-19), have become and provenance of its most recent ancestors, and sur- mired in politics, poorly supported assumptions and prisingly, the place, time, and mechanism of transmis- assertions, and incomplete information. sion of the first human infection. Even though a SARS-CoV-2 is a betacoronavirus whose apparent definitive answer may not be forthcoming, and even closest relatives, RaTG13 and RmYN02, are reported though an objective analysis requires addressing To avoid or mitigate the dire consequences of this and future pandemics (here, people in PPE bury a victim in Delhi, India in June), unraveling the origins of SARS-CoV-2 and COVID-19 will be essential—even though a definitive answer may be elusive, and an objective analysis means broaching some uncomfortable possibilities.
    [Show full text]
  • Unique Features Concerning the Proximal Origin of SARS-Cov-2
    Unique features concerning the proximal origin of SARS-CoV-2 Murat Seyran1,2, Damiano Pizzol3, Parise Adadi4, Tarek Mohamed Abd El-Aziz5,6, Sk. Sarif Hassan7, Antonio Soares5, Ramesh Kandimalla8,9, Kenneth Lundstrom10, Murtaza Tambuwala11, Alaa A. A. Aljabali 12, Amos Lal13, Gajendra Kumar Azad14, Pabitra Pal Choudhury15, Vladimir N. Uversky16, Samendra P. Sherchan17, Bruce D. Uhal18, Nima Rezaei19,20,*, Adam M. Brufsky21,* 1Doctoral studies in natural and technical sciences (SPL 44), University of Vienna, Austria. 2Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Austria. [email protected], [email protected] 3Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan. [email protected] 4Department of Food Science, University of Otago, Dunedin 9054, New Zealand. [email protected], [email protected] 5Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA. [email protected], [email protected] 6Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt. 7Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India. [email protected] 8CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad-500007, Telangana State, India. 9Kakatiya Medical College/MGM-Hospital, DME/TSPSC, Hyderabad, Warangal, Telangana State- 506007, India. [email protected], [email protected] 10PanTherapeutics, Rte de Lavaux 49, CH1095 Lutry, Switzerland. [email protected] 11School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK. [email protected] 12Department of Pharmaceutical Sciences, Yarmouk University—Faculty of Pharmacy, Irbid 566, Jordan 1 13Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota, USA.
    [Show full text]
  • The SARS-Cov-2 Genome: Variation, Implication and Application
    26 AUGUST 2020 The SARS-CoV-2 genome: variation, implication and application This rapid review describes the severe acute respiratory syndrome coronavirus-2 (SARS- CoV-2) genome, its relationship to other coronaviruses, the variation that has occurred since SARS-CoV-2 emerged in Wuhan in late 2019, the implications of these changes and how knowledge of these changes may be utilised. This pre-print from the Royal Society is provided to assist in the understanding of COVID-19. Executive summary • SARS-CoV-2 emerged in late 2019 in Wuhan, China. The • Whole genome sequencing is a valuable addition to test, genome of many separate virus isolates from early in the track and trace, and is encouraged. For instance it: Wuhan outbreak are very closely related showing the virus – has revealed >1350 separate introductions of SARS- emerged recently in humans. CoV-2 into the UK from mid-February to mid-March • The SARS-CoV-2 genome is sufficiently different to all 2020 arising very largely from Spain, France and known coronaviruses to refute the assertion that the Italy, and not from China. COVID-19 pandemic arose by deliberate or accidental – can be used to follow transmission within specific release of a known virus and make it highly improbable communities such as hospitals, schools or factories, that the virus arose by artificial construction in a laboratory. and combined with epidemiological data enables • SARS-CoV-2 is most closely related to bat coronaviruses routes of transmission to be identified and barriers from China, but even the closest of these viruses are too to transmission implemented.
    [Show full text]
  • Genetic Spectrum and Distinct Evolution Patterns of SARS-Cov-2
    medRxiv preprint doi: https://doi.org/10.1101/2020.06.16.20132902; this version posted August 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Genetic spectrum and distinct evolution patterns of SARS-CoV-2 Sheng Liu1,2 ¶, Jikui Shen3 ¶, Shuyi Fang4, Kailing Li4, Juli Liu5, Lei Yang5, Chang-Deng Hu6,7, Jun Wan1,2,4,8 * 1. Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA 2. Collaborative Core for Cancer Bioinformatics (C3B) shared by Indiana University Simon Comprehensive Cancer Center and Purdue University Center for Cancer Research, Indiana USA 3. The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA 4. Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University – Purdue University Indianapolis, Indianapolis, Indiana, USA 5. Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana USA 6. Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA 7. Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana USA 8. The Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA ¶ These authors have equal contributions. * To whom correspondence should be addressed. Tel: 1-317-2786445; Fax: 1-317-278-9217; Email: [email protected] Keywords SARS-CoV-2, single nucleotide variant (SNV), clustering, co-infection, evolution. Abstract Four signature groups of frequently occurred single-nucleotide variants (SNVs) were identified in over twenty-eight thousand high-quality and high-coverage SARS-CoV-2 complete genome sequences, representing different viral strains.
    [Show full text]
  • WHO-Convened Global Study of the Origins of SARS-Cov-2： Terms of References for the China Part
    Terms of references – FINAL DRAFT WHO-convened Global Study of the Origins of SARS-CoV-2： Terms of References for the China Part 31 July 2020 Contents Background ............................................................................................................................................ 2 Approach ................................................................................................................................................ 2 Current knowledge supporting origin tracing work ............................................................................... 3 Phylogenetic work.............................................................................................................................. 3 Animal susceptibility and animal surveys .......................................................................................... 4 Persistence of the virus on food and surfaces ................................................................................... 4 The early cluster in Wuhan ................................................................................................................ 5 Implementation plan ............................................................................................................................. 6 Phase 1: Short term studies ............................................................................................................... 6 a) Descriptive Epidemiological Study ........................................................................................
    [Show full text]
  • Evidence for SARS-Cov-2 Related Coronaviruses Circulating in Bats and Pangolins in Southeast Asia
    ARTICLE https://doi.org/10.1038/s41467-021-21240-1 OPEN Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia Supaporn Wacharapluesadee1,10, Chee Wah Tan 2,10, Patarapol Maneeorn3,10, Prateep Duengkae4, Feng Zhu 2, Yutthana Joyjinda1, Thongchai Kaewpom1, Wan Ni Chia2, Weenassarin Ampoot1, Beng Lee Lim2, Kanthita Worachotsueptrakun1, Vivian Chih-Wei Chen 2, Nutthinee Sirichan4, Chanida Ruchisrisarod1, Apaporn Rodpan1, Kirana Noradechanon3, Thanawadee Phaichana3, Niran Jantarat3, Boonchu Thongnumchaima3, Changchun Tu 5,6, Gary Crameri7, Martha M. Stokes8, ✉ ✉ Thiravat Hemachudha1,11 & Lin-Fa Wang 2,9,11 1234567890():,; Among the many questions unanswered for the COVID-19 pandemic are the origin of SARS- CoV-2 and the potential role of intermediate animal host(s) in the early animal-to-human transmission. The discovery of RaTG13 bat coronavirus in China suggested a high probability of a bat origin. Here we report molecular and serological evidence of SARS-CoV-2 related coronaviruses (SC2r-CoVs) actively circulating in bats in Southeast Asia. Whole genome sequences were obtained from five independent bats (Rhinolophus acuminatus) in a Thai cave yielding a single isolate (named RacCS203) which is most related to the RmYN02 isolate found in Rhinolophus malayanus in Yunnan, China. SARS-CoV-2 neutralizing antibodies were also detected in bats of the same colony and in a pangolin at a wildlife checkpoint in Southern Thailand. Antisera raised against the receptor binding domain (RBD) of RmYN02 was able to cross-neutralize SARS-CoV-2 despite the fact that the RBD of RacCS203 or RmYN02 failed to bind ACE2. Although the origin of the virus remains unresolved, our study extended the geographic distribution of genetically diverse SC2r-CoVs from Japan and China to Thailand over a 4800-km range.
    [Show full text]