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) h2. 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