《内科学》课程教学资源（新冠文献）Emerging novel coronavirus（2019-nCoV）current scenario, evolutionary perspective based on genome analysis and recent developments

Veterinary ④Tayr&Franc Veterinary Quarterly ISSN:0165-2176(Print)1875-5941(Online)Journal homepage:https://www.tandfonline.com/oi/tveg20 Emerging novel coronavirus(2019-nCoV)-current scenario,evolutionary perspective based on genome analysis and recent developments Yashpal Singh Malik,Shubhankar Sircar,Sudipta Bhat,Khan Sharun, Kuldeep Dhama,Maryam Dadar,Ruchi Tiwari Wanpen Chaicumpa 1&W (2019-nCoM current scenario,evolutiona tive based on g a9naysngneen developments.Veterinary Quarterly.40:1.68-76.DOl:10.1080016512020.1 To link to this article:https://doi.org/10.1080/01652176.2020.1727993 8 KmaingrmView supplementary material Group 自 乙Submit your article to this joul乙 Article views:5613 View related articles view crossmark data https://w

Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tveq20 Veterinary Quarterly ISSN: 0165-2176 (Print) 1875-5941 (Online) Journal homepage: https://www.tandfonline.com/loi/tveq20 Emerging novel coronavirus (2019-nCoV)—current scenario, evolutionary perspective based on genome analysis and recent developments Yashpal Singh Malik, Shubhankar Sircar, Sudipta Bhat, Khan Sharun, Kuldeep Dhama, Maryam Dadar, Ruchi Tiwari & Wanpen Chaicumpa To cite this article: Yashpal Singh Malik, Shubhankar Sircar, Sudipta Bhat, Khan Sharun, Kuldeep Dhama, Maryam Dadar, Ruchi Tiwari & Wanpen Chaicumpa (2020) Emerging novel coronavirus (2019-nCoV)—current scenario, evolutionary perspective based on genome analysis and recent developments, Veterinary Quarterly, 40:1, 68-76, DOI: 10.1080/01652176.2020.1727993 To link to this article: https://doi.org/10.1080/01652176.2020.1727993 © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group View supplementary material Accepted author version posted online: 08 Feb 2020. Published online: 27 Feb 2020. Submit your article to this journal Article views: 5613 View related articles View Crossmark data

ARY OL ©Ta&Franis SHORT COMMUNICATION OPEN ACCESS国 Emerging novel coronavirus(2019-nCoV)-current scenario,evolutionary perspective based on genome analysis and recent developments Yashpal Singh Malik.Shubhankar Sircar,Sudipta Bhat,Khan Sharun,Kuldeep Dhama Maryam Dadar,Ruchi Tiwari and Wanpen Chaicumpa ICAR-Indian /eterin e dia:bDivision ICAR-1 diar inary yPashu BSTRACT ses are the well-kr ARTICLE HISTOR 9 20o2-209i6o drom dby Middle East Re e co KEYWORDS 019-nCoV y of ir ational a ,30h Acute (nm the spread therapeutics:vaccines e threat of ghts ssful agnostics and effective vaccine 1.Introduction esult of its global spread(Kahn and Mclntosh 2005) Coronaviruses (CoVs)are well-known causes of virus was detected in the cagec severe infections,respiratory,enteric and systemic,in s and these were thought to humans and numerous animal hosts.The CoV infec be the natural host of this virus (Guan et al.2003) tions hav beer repo ted in cattle swine, Following SARS-CoV incidence in 2003,a similar Cov named HKU3-1 to HKU3-3 were identified in the horseshoe bats (non-caged)in 2005 from Hong and avian sp and Kong (Lau et al.2005). Since then,bats are consic Mcntosh 2005)The coronaviruses of relevant veter to be tr natural host and potential reservo nary species are shown in Table 1 with organ he affected and clinical signs.Though human CoVs 005)Afte 2003 2005 SARS-CoV e wer id in the year 19 tory as ch ged in the Middle illness and was named the Middle East Respiratory CoV (SARS-CoV)in the year Syndrome CoV (MERS-CoV)(Zaki et al.2012).The 2002-2003(Drosten et al.2003;Ksiazek et al.2003; mortality was higher than previous SARs-CoV pan Peiris et al.2003).In this SARS-CoV epidemic,around demic claiming around 919 lives out of the total 8000 confirmed human cases with 774 deaths 2521 human cases (around 35%mortality)(World (around 9.5%mortality rate)occurred that was a Health Organization 2015).Notably,dromedary nailcom:Kuldeep Dh 01652176.20191697012

SHORT COMMUNICATION Emerging novel coronavirus (2019-nCoV)—current scenario, evolutionary perspective based on genome analysis and recent developments Yashpal Singh Malika , Shubhankar Sircara , Sudipta Bhata , Khan Sharunb , Kuldeep Dhamac , Maryam Dadard , Ruchi Tiwarie and Wanpen Chaicumpaf a Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India; b Division of Surgery, ICAR–Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India; c Division of Pathology, ICAR–Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India; d Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran; e Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India; f Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand ABSTRACT Coronaviruses are the well-known cause of severe respiratory, enteric and systemic infections in a wide range of hosts including man, mammals, fish, and avian. The scientific interest on coronaviruses increased after the emergence of Severe Acute Respiratory Syndrome corona￾virus (SARS-CoV) outbreaks in 2002-2003 followed by Middle East Respiratory Syndrome CoV (MERS-CoV). This decade’s first CoV, named 2019-nCoV, emerged from Wuhan, China, and declared as ‘Public Health Emergency of International Concern’ on January 30th, 2020 by the World Health Organization (WHO). As on February 4, 2020, 425 deaths reported in China only and one death outside China (Philippines). In a short span of time, the virus spread has been noted in 24 countries. The zoonotic transmission (animal-to-human) is suspected as the route of disease origin. The genetic analyses predict bats as the most probable source of 2019-nCoV though further investigations needed to confirm the origin of the novel virus. The ongoing nCoV outbreak highlights the hidden wild animal reservoir of the deadly viruses and possible threat of spillover zoonoses as well. The successful virus isolation attempts have made doors open for developing better diagnostics and effective vaccines helping in combating the spread of the virus to newer areas. ARTICLE HISTORY Received 3 February 2020 Accepted 6 February 2020 KEYWORDS Coronavirus; 2019-nCoV; Severe Acute Respiratory Syndrome CoV; Middle East Respiratory Syndrome CoV; Public Health Emergency; genetic analyses; zoonoses; reservoir host; therapeutics; vaccines 1. Introduction Coronaviruses (CoVs) are well-known causes of severe infections, respiratory, enteric and systemic, in humans and numerous animal hosts. The CoV infec￾tions have been reported in cattle, swine, horses, camels, rodents, cats, dogs, bats, palm civets, ferrets, mink, rabbits, snake, and several other wild animals and avian species (Fehr and Perlman 2015; Kahn and McIntosh 2005). The coronaviruses of relevant veter￾inary species are shown in Table 1 with organ affected and clinical signs. Though human CoVs were identified for the first time in the year 1960 from respiratory infections in adults as well as chil￾dren, the major scientific interest in CoVs research grew only after the emergence of Severe Acute Respiratory Syndrome CoV (SARS-CoV) in the year 2002-2003 (Drosten et al. 2003; Ksiazek et al. 2003; Peiris et al. 2003). In this SARS-CoV epidemic, around 8000 confirmed human cases with 774 deaths (around 9.5% mortality rate) occurred that was a result of its global spread (Kahn and McIntosh 2005). Initially, the virus was detected in the caged Himalayan palm civets and these were thought to be the natural host of this virus (Guan et al. 2003). Following SARS-CoV incidence in 2003, a similar CoV named HKU3-1 to HKU3-3 were identified in the horseshoe bats (non-caged) in 2005 from Hong Kong (Lau et al. 2005). Since then, bats are consid￾ered to be the natural host and potential reservoir species that could be held responsible for any future CoVs epidemics and/or pandemics (Cui et al. 2019, Li et al. 2005). After the 2003 and 2005 SARS-CoV epi￾demics, an analogous virus emerged in the Middle East region of the world leading to severe respiratory illness and was named the Middle East Respiratory Syndrome CoV (MERS-CoV) (Zaki et al. 2012). The mortality was higher than previous SARS-CoV pan￾demic claiming around 919 lives out of the total 2521 human cases (around 35% mortality) (World Health Organization 2015). Notably, dromedary CONTACT Yashpal Singh Malik malikyps@gmail.com; Kuldeep Dhama kdhama@rediffmail.com; Wanpen Chaicumpa wanpen.cha@mahidol.ac.th Supplemental data for this article is available online at https://doi.org/10.1080/01652176.2019.1697012.
2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. VETERINARY QUARTERLY 2020, VOL. 40, NO. 1, 68–76 https://doi.org/10.1080/01652176.2020.1727993

VETERINARY QUARTERLY④6的 Table1.Coronaviruses of relevant veterinary spece Host Genus Organ affectec Clinical sign tory tra ory disease c pp Porcine diarrhea nica is and diarrhea Canine anheceorpar5oonsis ory tract Chicken Decreased egg productio camels were connected with the transmission of has been noted in 24 countries till date.Considering MERS-CoV (Alagaili et al.2014).Further,its origin was the global threat of the 2019-nCoV,the World also traced from bats (lthete et al.2013).All these Health Organization (WHO)declared it as a Public highly pathogenic nan Cov RS and MERS,show Health Emergency of International Concern'on -to areas or the uary s anid es thereto (Figure 1). of the recently emerging coronavirus (2019-nCov This decade's first Cov emergency was from with regards to its current scenario,comparative Hubei province of China,and as on February 4, analysis with respects to previously reported CoVs nave bee b) China only nary pe e d of ad 2018-ncov rief

camels were connected with the transmission of MERS-CoV (Alagaili et al. 2014). Further, its origin was also traced from bats (Ithete et al. 2013). All these highly pathogenic human CoVs, SARS and MERS, show emergence over wider areas of the world posing high risk of human-to-human transmission and fatal conse￾quences thereto (Figure 1). This decade’s first CoV emergency was from Hubei province of China, and as on February 4, 2020, 425 deaths have been reported in China only (World Health Organization 2020b). Further, the spread of this novel coronavirus, named 2019-nCoV, has been noted in 24 countries till date. Considering the global threat of the 2019-nCoV, the World Health Organization (WHO) declared it as a ‘Public Health Emergency of International Concern’ on January 30th, 2020. This rapid communication provides an overview of the recently emerging coronavirus (2019-nCoV) with regards to its current scenario, comparative analysis with respects to previously reported CoVs, evolutionary perspective based on genome analysis while covering the recent advances on vaccines and therapeutics in brief. Table 1. Coronaviruses of relevant veterinary species. Host Virus Genus Organ affected Clinical sign Bovine Bovine coronavirus Betacoronavirus GI Tract Respiratory tract Calf diarrhea Winter dysentery (bloody diarrhea) in adult cattle Bovine respiratory disease complex (shipping fever) Porcine Transmissible gastroenteritis (TGE) virus Alphacoronavirus GI Tract Profuse watery yellow diarrhea, Vomition, dehydration Porcine respiratory coronavirus Alphacoronavirus Respiratory tract Mild respiratory disease or subclinical Porcine epidemic diarrhea virus (PEDv) Alphacoronavirus GI Tract Watery diarrhea, vomition, dehydration Porcine hemagglutinating encephalomyelitis virus Betacoronavirus GI Tract CNS Vomition, Diarrhea Wasting disease Encephalomyelitis Porcine deltacoronavirus Deltacoronavirus GI Tract Gastroenteritis Feline Feline enteric coronavirus Alphacoronavirus GI Tract Mild gastroenteritis and diarrhea Feline infectious peritonitis virus Alphacoronavirus Respiratory tract Abdominal cavity CNS Pneumonia Peritonitis Neurological disorder Canine Canine coronavirus Alphacoronavirus GI Tract Mild to severe gastroenteritis Canine respiratory coronavirus Betacoronavirus Respiratory tract Kennel cough Pneumonia Equine Equine coronavirus Betacoronavirus GI Tract Gastroenteritis Camel Middle East respiratory syndrome (MERS) coronavirus Betacoronavirus Respiratory tract Mild respiratory signs Chicken Avian infectious bronchitis virus Gammacoronavirus Trachea Kidney Reproductive tract Tracheobronchitis, Rales Nephritis Decreased egg production Figure 1. World-map depicting countries with SARS-CoV and MERS-CoV outbreaks. Red and yellow colors represent the global distribution of only MERS-CoV and SARS-CoV, respectively. The yellow-red dotted pattern shows the incidence of both viruses in the countries. VETERINARY QUARTERLY 69

70Y.S.MALK ET AL 2.Coronaviruses the Chinese Center for Disease Control and Prevention (CDC)that a new coronavirus has emerged and wa 95 named 20 idae and the order single-stranded positive-sense rNa genome ranging ere cases of 2019-nCoV.In addition to China,24 dif from 26 to 32kb in length(the largest genome of ferent countries from Europe,Northern America known RNA viruses)with G+C contents varying from Southeast Asia,Eastern Mediterranean,and Westerr 32to43% ic structure ana phylo dis cas gene Betacoronavirus. and 2019nC the earlier outbreaks of SARS and MERS-CoVs,as Deltacoronavirus.Among these Alphacoronavirus and as this virus presents relatively mild manifestations ronavirus infects only ma the total number of cases are increasing speedily and are cros ssing the old census.There is a high risk of ruses.SARS-CoV and MERS-CoV belong to the g um wh as als Betacoronavirus.The genus Betacoronavirus further mily distributed in five subgenus among which ea with hest radiographs show g acute inva e Groot sive lesions in both lungs. ,2012 Hihe The nCov contains at least six open reading frames (ORFs)and many other accessory genes like other Currently.knowledge about the origin of the viru (ORFs its particular receptor,clinical spectrum and host ecies preference is unknown.World over scientists which is further ceaved into 11 and 16 aged in unraveling th e genomi nature o respectively.These 16 mature proteins are responsible now,aro 15 for several important function nCoV genom 5 USA) ance and ruc usage analysis speculated snakes to be its natural (E)mem host,whereas several subsequent reports after that one-third a'to mminal of the a ome In addition to oublication rejected this hypothesis They found the members to be Bat_SARS-like CoVs (Bat-SL 5,N lysis 34)in phylogenetic ana the most important genes for receptor binding and HE)om 4.1.Analysis targeting the complete genome of 2019-nCoVs 3.The emergence of novel-Coronavirus also atte (2019-nco) npted to reveal the of th 201g During the first week of Dec the complete Hube Phylogenetic analysis was done using the MEGA 7.0 province of China.The patients exhibited a history of applying the Maximum likelihood method visiting the local nearby Huanan seafood market ML Reversible substitutio which deals in the sale of different live the where zoo anima 201 28h2020 of th 2020).Firstly,the affected patients pre nted witl urrent 2019-ncoy outbreak sequences as calc pneumonia-like symptoms,followed by a severe lated using the MegAlign software of DNASTAR.In acute respiratory infection.Some cases showed rapid whole genome phylogenetic analysis,the 2019 cute respiratory distress syndrome CoV strains s from China and the USA clustered in a ARDS) h

2. Coronaviruses Coronaviruses (CoVs) constitute a large family of viruses found in nature. CoVs belongs to the family Coronaviridae and the order Nidovirales possessing a single-stranded, positive-sense RNA genome ranging from 26 to 32 kb in length (the largest genome of known RNA viruses) with G þ C contents varying from 32 to 43%. Based on the genomic structure and phylo￾genetic analysis the subfamily Orthocoronavirinae con￾sists of four genera namely Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. Among these Alphacoronavirus and Betacoronavirus infects only mammals and are respon￾sible for respiratory infection in humans and enteritis in animals. Two major zoonotic pathogenic coronavi￾ruses, SARS-CoV and MERS-CoV belong to the genus Betacoronavirus. The genus Betacoronavirus further distributed in five subgenus among which Sarbecovirus contains SARS-CoV and the novel corona￾virus (2019-nCoV) (de Groot et al. 2012). The other subgenera under Betacoronavirus are Embecovirus, Hibecovirus, Merbecovirus, and Nobecovirus. The nCoV contains at least six open reading frames (ORFs) and many other accessory genes like other CoVs. The 50 terminal two-thirds of the genome con￾tains two open reading frames (ORFs), ORF1 and ORF2 which encodes two polyproteins, pp1a and pp1ab, which is further cleaved into 11 and 16 proteins, respectively. These 16 mature proteins are responsible for several important functions in genome mainten￾ance and virus replication. The structural proteins namely spike (S), an envelope protein (E), membrane protein (M) and nucleocapsid (N) are located at the one-third 30 terminal of the genome. In addition to these genes, there are several accessory proteins which help in virus replication. The S gene is one of the most important genes for receptor binding and host specificity. Some coronaviruses have hemagglu￾tinin-esterase (HE) protein in their virion. 3. The emergence of novel-Coronavirus (2019-nCoV) During the first week of December 2019, a few cases of pneumonia appeared in the city of Wuhan, Hubei province of China. The patients exhibited a history of visiting the local nearby Huanan seafood market which deals in the sale of different live animals, where zoonotic (animal-to-human) transmission sus￾pected as the main route of disease origin (Hui et al. 2020). Firstly, the affected patients presented with pneumonia-like symptoms, followed by a severe acute respiratory infection. Some cases showed rapid development of acute respiratory distress syndrome (ARDS) followed by serious complications in the respiratory tract. On Jan 7th, 2020, it was confirmed by the Chinese Center for Disease Control and Prevention (CDC) that a new coronavirus has emerged and was named 2019-nCoV. As on February 4th 2020, China has confirmed 20471 cases with 425 deaths and 2788 severe cases of 2019-nCoV. In addition to China, 24 dif￾ferent countries from Europe, Northern America, Southeast Asia, Eastern Mediterranean, and Western Pacific Asia have reported the confirmed cases of this disease making the total tally of confirmed cases to 20630 worldwide (Figure 2). Although the mortality rate due to 2019-nCoV is comparatively lesser than the earlier outbreaks of SARS and MERS-CoVs, as well as this virus presents relatively mild manifestations, the total number of cases are increasing speedily and are crossing the old census. There is a high risk of human-to-human transmission which has also been reported in family clusters and medical workers. The infected patients with nCoV exhibit high fever and dyspnea with chest radiographs showing acute inva￾sive lesions in both lungs. 4. Phylogenetic analysis and sequence identity Currently, knowledge about the origin of the virus, its particular receptor, clinical spectrum and host species preference is unknown. World over scientists are engaged in unraveling the genomic nature of this virus. As of now, around 15 complete 2019- nCoV genome sequences (10 China and 5 USA) have been reported. To note, a report based on the codon usage analysis speculated snakes to be its natural host, whereas several subsequent reports after that publication rejected this hypothesis. They found the nearest members to be Bat_SARS-like CoVs (Bat-SL￾CoVs, MG772933 & MG772934) in phylogenetic ana￾lysis within the subgenus Sarbecovirus. 4.1. Analysis targeting the complete genome of 2019-nCoVs In this study, we also attempted to reveal the evolu￾tionary perspective of the recently emerging 2019- nCoV based on the complete genome analysis. Phylogenetic analysis was done using the MEGA 7.0 version applying the Maximum likelihood method (ML) based General Time Reversible substitution model with the available whole genome sequences of 2019-nCoV available in the NCBI GenBank data￾base till January 28th, 2020. Pairwise identity of the current 2019-nCoV outbreak sequences was calcu￾lated using the MegAlign software of DNASTAR. In the whole genome phylogenetic analysis, the 2019- nCoV strains from China and the USA clustered in a monophyletic clade (Figure 3). The nearest neighbors of the 2019-nCoV isolates from China and USA were 70 Y. S. MALIK ET AL

VETERINARY QUARTERLY(⊙刀 med Cases igure 2. ted confim edepicted. of 2019-nCo two Bat_SARS-like coronaviruses (Bat-SL-CoVZC45, identical to the bat coronavirus based on Simplot Accession no. MG772933 and Bat-SL-CoVZXC2 analysis where it has been found closer to bat Cov Accession no.MG772934).These two Bat_SARS-like solate RaTG13 previously detected in Rhinolophus otstrap s oport with 2015 norse noe ba ron na Pd MEGA 7O the ba alignments,the nucleotide sequence identity of ather early to r predict the orioin of this novelcoron 2019-nCov strains revealed the highest similarity of virus without a comprehensive analysis of emerging greater than 88.2%with two Bat_SARS_like Covs. nCov strains from different parts of the world.To hese findings were in accordance with report of Zhu note,the sequence identity based on the complete genome sequences between current outbreaks 2019 Bat_SARS V I eniepoeaobe96s evel

two Bat_SARS-like coronaviruses (Bat-SL-CoVZC45, Accession no. MG772933 and Bat-SL-CoVZXC21, Accession no. MG772934). These two Bat_SARS-like CoVs shared a 100% bootstrap support with 2019- nCoV strains of the current outbreak. Using the MegAlign and MEGA 7.0 software based Clustal W alignments, the nucleotide sequence identity of 2019-nCoV strains revealed the highest similarity of greater than 88.2% with two Bat_SARS_like CoVs. These findings were in accordance with report of Zhu and colleagues where a nearby sequence identity of 86.9% with previously published Bat_SARS-like CoV was reported (Zhu et al. 2020). Contrarily, the gen￾ome of 2019-nCoV has also been reported to be 96% identical to the bat coronavirus based on Simplot analysis where it has been found closer to bat CoV isolate RaTG13 previously detected in Rhinolophus affinis (intermediate horseshoe bat) from Yunnan Province, indicating its origin from the bats (Zhou et al. 2020). Based on the available information it is rather early to predict the origin of this novel corona￾virus without a comprehensive analysis of emerging nCoV strains from different parts of the world. To note, the sequence identity based on the complete genome sequences between current outbreaks 2019- nCoV isolates from China and the USA ranges 99.8 to 100% on the nucleotide level indicating their com￾mon origin of evolution. Figure 2. Countries, territories or regions with reported confirmed cases of 2019-nCoV, February 4th, 2020. Different colors indicate different geographical regions with the number of confirmed cases. In the table, region-wise total number of con￾firmed cases are depicted. Figure 3. Phylogenetic analysis of 2019-nCoV isolates using complete genomes. The 2019-nCoV isolates analyzed with related CoVs from past human outbreaks and of animal origin. The solid-black circles are for nCoV isolates from China and solid-black squares are for the isolates from the USA. VETERINARY QUARTERLY 71